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||||| System Bio - Bio-Process- xOmes; Organ; Cell; OrganelleVehicle; Factory; Machines; Pathway; Motor-Molecule; Domain; Bond ||||| 

Agonist-Antagonist; Inhibitors; Toxic Proteins
Databases-Disease-Vaccines-Biodefense-HIV-DrugDiscovery -Gene Therapy-Journals-SARS
Top 100 Methods: Material; Protocols; Software; Viewers; Vectors; Vendors
Genome-Annotation-DB-Help; DNA-Repeats-Introns-Defense SNP-Evolution; other Omes
 Mutagenesis-DNA shuffling-CompareCis-Elements
 RNA & RNAi
Proteome; HDS/HTS; GFP/xFP
     Arrays: DNA; Protein 1; Small molecule; Frozen Cell; Transfected Cell

  Collaborate; Courses; Textbooks; Tutorials-FAQ-Guides; Development Cinema; elegans Cinema; Pathpicturesway Picture

|||BioPharma; Consortiums; Patents NCRR; Departments; Labs; Researchers; Publishers; Societies; Other Groups|||

Career - Transition; Authorship; Writing; Publishing; Funding; Mentoring; Science Education
||Commentary; History; Quotation; Profile; Exhibits ||

Announcements; Feedback; Introductions

  Vanderbilt; NASHVILLE

 

 
 

 

Top 100 Material & Methods

Bacterioph. b-gal/GFP
Bicistronic Bioluminesce
Cell Culture Cells- Parts
ChIP Cloning-M
Cloning-N CPE Assay
Chromium Release Consomic mouse
Consomic Strains CTL Assays
Cytogenetic DNA Ligase
Dir. Evolution DNA Extraction
DNA Methyl. DNA Polym.
DNA Restric DNA Repli.
EISA DNA Shuffle
ELISPOT Epigenetics
FACS F-L cDNA
FRET Gene Gun
Gene KO Gene Trap
Genetic Code Gene Silencing
Gene Therapy Genotyping
GFP||Camera
GFP/b-gal GFP/RFP Co-exp
Haplotypes Homologous Recombination
HTS Knockout Mouse
Linkage disequilibrium
Microarrays Mutagenesis
PCR
PCR DNA Pol PCR real-time
PCR-Race Phage display
Proteomics Protein  Chips
RFP RestrictionMapper
RNA Rolling-circle Am
RNAi - Dicer Run-On Transc.
Sequencing I Sequencing II
Separation Si/tRNAs
SNP SOE PCR
Sorting Tetramer Assay
Spectroscopy Transfection
Two-Hybrid Three-Hybrid
Vaccines Vectors
NAR links  

Departments

Anatomy Big Pic. Biol.
Cardiovascular
Chemistry Comput.Biol.
Development Dev.Biol|Cinema
Drug Discov. Gene Annot
Gene Ontolo. Gene Therapy
Immunology Medicine
Microbiology Neurobiology
Organis Biol. Physics
Systems Biol. Virology
Groups-BioPharm-Regulatory
Alliances Associations
ATP Bio-Computing
BioPharm Career
Consortiums Foundations
Funding NCRR
NIST Organizations
Patents Publishers
Institutes Societies

Model Organism 

C. elegans Chick
Cnida Dicty  Fly
Hum   Mou Nemat  Neuros.
Plant  PFish Rat  SeaU
Weed Xeno   Yeast  Zfish

Biological Process  

5'-End Form. 3'-End formation
Acetylation Adhesion 
Aging Antig-Cell
Apoptosis Antig-Present.
Autoimunity Antig-Proces
Cell Cycle Bug Detection
CC Progress Cell plasticity
Chemorecep.
Class Switch Cell-Specificity 
Coactivation Corepression
Competition Cross-Prime
Deacetylation Development
DNA Meth. DNA Repair
DNA Repl. Endocytosis
Endocytosis-Ubiquitin
Endosome Traf.
Enhancement Export mRNA
Gene Imprinting
G0 Silencing G0-G1 Transit
G0-G1 Transit 2
G1-S Transit G2-M Transit
G-Nuc-Bind Gluconeogenesis
Glycosylation Histone Acet.
Histone H3 phosphorylation Hist. Modif.
Hypoxia Histones-DNA
HS Immune deficiency
Immunity Link
Imprinting Interactomes
LCR Inflammation
Memory Life-or-death
Memory Cells Methy. Imprint
Modular Feedback Nitrosylation
Nuclear Anchoring Nuclear breakdown 
Nuclear entry Nuclear Export
Nuc Herniation Nuclei Tetherin
Oncogenic TF
Operome O2 Signaling
Oxidant Stress Path Pictures
Quorum sensing Phagosytosis
Phenome Physiome
Proofreading Prot. Degrad
Prot. Degrad & Cell Cycle
RAR Synergy Protein-DNA
Prot. Methyl. Protein-Prot.
RNA Splicing Redox Sensor
Scaffolding Secondary Responses
Senescence Signal duration
Signal Trans Silencing-RNA
Sleep Silencing-methy
Silencing Suppression
Speech Splicing regulati
Synexpression Tissue-Specific
Transcription Transc_Export
Transl. Reg. Trans-splicing
Translation Transport N|C
Ubiquitin Removal
Vesicle Traf. Ubiquitylation

Organ Biology

Bone Brain
Chemosens. Heart
Immune Sys. Kidney
Liver Mammary
Muscle Pancreas
Reproduction Respiratory

Cell

B Cells
CTL Dendritic
NK Stem-Orienting
T Th I & II

Organelle

Aggresome Caveolae
DALIS Desmosomes
Endosome 1 Endosome 2; M
Exosome Genome
Golgi biogene. Lysosome
Membranes Mitochondria
Nucleus Nuclear Anchoring
Peroxisome

Vehicle

Argosomes POD

 Factory

Gene Expression  

Machines

Chromatin Assembly & Remodeling Protea -somes
   

Motor

Dyneins Kinesin (Movies)
Myosin Prestin

Molecule - Complex - Function

7SK Agrin
Alu Repeats
Antimicrobials APIS
asRNA Artemis-DNA-PKcs
Calcium Caspase-8
Caveolin Calcium channel
Centromere Calreticulin
Chaperones Chemokines
Cdk-cyclin  k. Chromatin
Cholesterol Cis Elements
Clatherin C.P.
Coactivator Coact. Complex
CRSP/ARC-L Conn. T. Protein
Cohesin Corepressor
CYOxidase
CYP450 Cytokines
DNA-Protein DC-SIGN
EG-VEGF Enhanceosome
Ephrins Epsin
ERK Exosome
Exocyst Fibronectin II
Globin GILT
Glutamate Receptor
GPCRs G Proteins
GTPase Cycle GTPase Rho
GTPase Ran GTP-Binders
Helicase HP1
Hypocretin Heterochromatin
ICAM-3 IFN-g
IFN-a IKK
IL-1 Receptor IL-23
Immun Synapse Integrin
Introns Ion Channels
IP3 - DAG JNK
Insulasomes Lymphokines
MAPK Mediator
MHC I &  II Methyltransferase
miRNA Muscle Proteins
NF-kB Non-code RNA
Nrd1 Na Channel
Nuclear Recept
Nucleic Acid Nucleoporin
Nucleosome Oncogenic TF
p53 PI3K
Peptide Nucleic Acid
Poly(A) polymerase Preinitiation C
Prot. Degrad Protein-Prot
Protein-DNA Protea -somes
RAR  Pyr Dehydog
Reelin P-TEFb
Ribosome Ribozyme
RNA RNA Helicase
RNA Poly I RNA Poly II
snRNA Silencesomes
Sos-ras Spliceosome
SRF Steroids
TAP I & II T-bet
TAFs TCR
Telomerase Termination
TFIID TGF-b
tmRNA Transp. ABC
Transplantation  Toll-like Recept
TK.Receptor Transcriptome
Transporters Ubiquitin-Endo
Ubi-Pr-VCP
Ubiquitin Ligase Ubiquitin-Trans

Toxic Proteins

Neuro-degenerative Toxins-Antitoxins

Domain - Motif

Anth Argonaute
Bromdomain Cluster Desig.
Chromodomain Chromoshadow
Degrons DEF
Enth Flap-Polymerase
Forkhead FXFP
HECT Helicase
NLS PAZ 
PGRP PIWI
POD Polo-box
PTEN RING Finger
SET T-box
TIR U Box
UIM Zwille

Pathways & Pictures

Agonist-Antagonists

SERMs

Inhibitors

MMPs

Disease

Asthma Diabetes
  Huntington's
Malaria Parkinson's
  Smallpox - More
Werner Synd. Others

Commentary, History,  Profile,  & Exhibits

Bioinformatics Cell Biology
Chemistry Genetics
Genome Science

Virology

WWW

         ||||||||||||||||||||||||||||||||||||||||

          |||||||||||||||||||||||||||||||||||EX

Mail Phone Books Travel

INTRODUCTION

Bioinformatics ---

Weizmann Institute

Indiana University

Rensselaer Polytechnic Institute

India.com

Clinton-Gore Admin.

  • Bioinformatics in the 21st Century - A Report to the Research Resources and Infrastructure Working Group Subcommittee on Biotechnology National Science and Technology Council White House Office of Science and Technology Policy.
Amphibians
Cells-Molecules-Organisms
Discoideum
Nematodes
Sea Urchin

Yeast

Cis ELEMENTS
DATABASES-ciselemments

SERVICES -ciselemments

PROJECTS-ciselemments

||||Cis elements@Wheaton College

PORTALS (more links)-ciselemments

RNA & RNAi Worlds
RNAi@elegansNet

Reviews

Literature

Databases

Cinema elegans  - Includes:

RNA WORLD
Clubs RNA

Databases RNA

Commercial Sites RNA
Databases (Scottish RNA Club; MRC, UK). dbrnaworld
Journal RNA

Informatics RNA

Informatics (Scottish RNA Club; MRC, UK).
  • Analysis (Institut Pasteur
  • Draw - Matzura & Wennborg (ole@mango.mef.ki.se).
  • Informatics (Stanford, CA, USA).
  • mfold - Michael Zuker, (Wash. U., St. Louis, MO, USA).
  • Modeling - (Biochemistry and Molecular Genetics, U. Alabama, USA).
  • Ribosomal Database Project (RDP) provides ribosome related data services including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences
  • RNA Editing - Larry Simpson (UCLA, USA).
  • RNA GENiE - locates novel RNA genes based on the premise that all stable....(Rich Carter)
  • Vienna RNA Package by ilh - A free software package for RNA secondary structure analysis. Offers libraries and programs for calculation of minimum free energy structures, suboptimal structures, and base pair probabilities, structure comparison, and inverse folding.
  • World (IMB, Jena, Germany).
Labs RNA
  • Altman Group - RiboWeb by badaboy_99 - An ontology-based knowledge base, software components that test for
     
  • Beggs -Pre-mRNA splicing in yeast.
     
  • Brown by jwbrown42 - Structure, function, and evolution of RNase P, particularly in Archaea.
  • ChetverinViral RNA Biochemistry by - Studies on RNA recombination and Molecular Colony Technique that provides nucleic acid-based diagnostics, and for cell-free gene cloning, expression
  • Doudna - x-ray crystallography and biochemical techniques to study structure, mechanism and evolution of both ribozymes and RNA-protein complexes.
  • Holbrook: RNA Structure & Ribonomics - Structure and function of RNA and RNA-protein complexes; x-ray crystallography and computational methods, neural networks
  • Krug - Regulation of processing (splicing and 3' end processing) and nuclear export of cellular and viral mRNAs in virus- infected cells
  • Lamond - Pre-mRNA splicing and nuclear organization in mammalian cells.
  • MacMillan Research Group Homepage by ammacmill - Biochemical and chemical mechanisms of RNA processing
  • Martin Holcik's by mholcik2001- The regulation of translation during apoptosis and other cellular stresses
  • Misteli - Research is to uncover how genes are expressed in living cells.
  • Linderpatrick - RNA helicases from yeast - This site is a compilation of data on RNA helicases from yeast, with emphasis on DEAD-box proteins
  • Sachs - Links to it's publications and other useful sites
  • Sarnow - Links to papers, people and science sites.
  • Singer - Using in situ hybridization, we visualize specific nucleic acid sequences within individual cells.
  • Terns - Metabolism, transport, and function of cellular RNAs,
  • Tollervey by tollervey Synthesis and degradation of many different types of RNA depends on a set of common nucleases and cofactors.
  • Vester RNA group - RNA footprinting of ribosome specific antibiotics, Mapping of posttranscriptional modifications of 23S ribosomal RNA..
  • Wilson - RNA structure-function relationships using RNA aptamers and biological RNA- protein complexes, x-ray crystal structure coordinates for var
Meetings R

Methods RNA

Methods RNA Methods
Miscellaneous RNA

RNA Webring

Portals RNA
RNA Webring - provides links between many of the molecular biology institutions and private companies that have an interest in any aspect of RNA metabolism.

Back to RNA & RNAi Worlds

  Splicing

 

Heart
Reviews

   NATURE, 415, 197-243, 2002

  • Cardiac excitation contraction coupling
  • Seven transmembrane -spanning receptors and heart function
  • Cardiac channelopathies
  • New ideas about atrial fibrillation 50 years on
  • The failing heart
  • Myocardial gene therapy
  • Myocyte renewal and ventricular remodelling
GFP - RFP - xFP
New

Main GFP Pages

GFP-Probing Gene Expression (UMBC, Jincai Li)

Material & Methods GFP

News Group GFP

Quantitation & ScreeningGFP

References GFP

Sensitivity GFP

Vendors GFP

TLRTOLL-LIKE RECEPTOR
TOLL-LIKE RECEPTORS
Reviews

TLRs & Imd

Subunit Interactions

 
DNA POLYMERASES & PCR
 ABC of DNA Polymerase in PCRrase

Which polymerase & when?

Selected PCR Polymerases

DNA SHUFFLING - Directed Evolution; Sexual PCR; Family Shuffling; Molecular Breeding; Sexual PCR
ABC Shuffle

Publications shuffle

Shuffle Variants

  • DOGS - Gibbs et al. Gene 271 (2001) 13-20
  • RPR - Random Priming Recombination - Shao et al. NAR 26, 681-683 (1998)
  • RACHITT - Enchira
  • RM-PCR - No homology needed.
  • SCRATCHY - Homology independent; PNAS 98, 11248-11253 (2001)
  • StEP - staggered extension process - Nat. Biotechnol. (1998)16:258-261.

Labs shufflings

Examples - Summaries enzshuf

SPECTROSCOPY
 
CHEMISTRY & PHYSICS

Chemistry & Physics Topics (Dave Young's + elegansNet)

Directories ChemPhysics

Manuals Chemistry

Periodic Tables

IMMUNOLOGY

Basic Immunology

Databases Immunology

Labs - Immunology

MHC

Immunological Synapse

PROTEOMICS
Chips proteomics

Databases & Tools p&roteomics

Data Standard

Standards at last!

Interactomes

Portals proteomics

  • ProteomicsSURF - A proteomics directory of  methods & protocols for novice and advanced users. Also included are links to Bioinformatics, Genomics, Microarrays, PCR, Crystallography, NMR, & Chromatography.

Protein Reviews

  • PROW: Search Protein Reviews On the Web is an online resource that features PROW Guides, authoritative short, structured reviews on proteins and protein families.

Search proteomics

Societies proteomics

Mutagenesis
Methods mutagenesis

Databases

Locus Specific Mutation

Disease Centered Central Mutation

Central Mutation & SNP

National & Ethnic Mutation

Chromosomal Variation

Clinical & Patient Aspects

Non Human Mutation

Artificial Mutations Only

Other Related Databases

Education Resources for Teachers & Students

 

 
ANNOUNCEMENTS

elegansNet

C. elegans

Discoideum
Fly Fly

SEARCH ENGINES

Vivisimo

Search Tips:

Entrez Entrez Blast EpiVax GenBank EC Enzyme ExPASy HIV HUGE NCBI Owl PDB PIR Proteome Incyte; pfam Proteome@EBI Protein Reviews  Sanger Centre Genome DB WormBase

  for assembling disease-gene citation matrices from over 11 million Medline records, with relationships normalized into rank order.

HWJ  BMC PubMed Scirus BioTechniques  SciAm

GENES2000

 Dev. Biol. Society; Gilbert_dev.- Biol. Textbook

BioExplorer; BioNetbookBioHunt; BioWurld; Virtual Library

Bionet: Archive Google Fluorescent Proteins fly elegans mouse yeast Zfish

NIH NSF Gov COS CRISP

National Achieves & Records
Search for biological, chemical, drug, or book
Chemical & Physical DATA
Quotations Page; Quoteland Quotations Archive; Creative Quotations; Bartlett; Visual Thesaurus

knowledgebase: MS Adobe

Patents: Delphion; DNA; EPO; Micro; U.S.

BioPortfolio; Hoover's

Movies MagPortal Sounds

Google Fast Lycos

Adobe OpenDir AOL Yahoo

Searchcom AltaVista HOTBO

Metacrawl NorthernL More

Patent Search

Search elegansNet:

  • Browse topics at the top of this frame (Index Frame/Research Menu)
  • Or, use your browser's 'Find' key to navigate to link of interest (click your mouse in this frame, hold down Cntl + F on the key board, and in the Find dialogue box that appears type your search word). This method allows for most thorough & up to date search;
  • Or, search for pages available at  elegansNet by using PicoSearch engine on the main frame.   PicoSearch crawls this site every time elegansNet is updated, assuring most up to date searches.
  • Or, search for pages available at elegansNet by selecting the elegansNet radio button of Google search engine,  in the main frame
Search for biological, chemical, drug, or book
CGC obtain nematode strains & lookup researchers' address (C. elegans genetic center).
Chemicals? Find out which companies produce it, its chemical properties, and obtain safety sheets (Vermont SIRI MSDS Collection).
Chemical Safety Information
MedlineExtensive biochemical & drug information. Includes medical encyclopedia (NLM; 5/3/00).
Clinical Pharmacology - Drug search & more Merck Manual of Diagnosis and Therapy
Medscape - Drug, news, literature search & more. Books - Identify distributors & best prices. Bublos; Amazon; Fetchbook.info
Chemical & Physical DATA
Webmolecules - View Your favorite molecule form db of 21,000 (Molecular Arts Corp.).
Wired Chemist
Chemistry Web Book - Easily searchable (NIST):
Entropy on the World Wide Web - promotes appreciation of entropy in its many forms
More biomedical searches
American Medical Ass. BioNetbook (Institut Pasteur)
ClinicalTrials COS;CDL
Deja Institut Pasteur
Mayo NCBI
MedNet NIH
Searchlight STKE
Vanderbilt
More
Special Search Engines
About AOL

Chubba

Dogpile
Fast Excite
GO GOTO
ixquick Jeeves
LookSmart Lycos
NBCi Open directory
PortalSurfer ProFusion
Search.com SearchWho

MEETINGS
C. elegans Meetingscelegans
Other

Drug Discovery Meetings

Microarrays meetings

Pediatrics

Proteomics meetings

Vaccines DNA


Meeting Finders & Planners
Meeting Reports

Meeting Reports (BioMedNet)

NEWS/MEDIA
BioMed News by Media
Bioinformatics, Biotech, Pharm
Daily Research Highlights:

Special BioMed News Sources:

NIH & NSF
Signal Transduction News
Vanderbilt News

Bionet News Groups

All Archives: C. elegans; Fly; Yeast; Zebrafish

celegans & to Subscibe

drosophila

Gene/ Chromatin Structure

molbio.ageing

molbio.yeast

Mouse E-mail Bulletin

organisms.zebrafish

users.addresses


LITERATURE

Search Literature
Specific Journals
Journals - Access to Many
Essays & Reviews
elegansNet Selected
C. elegans related
Journal Abbreviations - JA abbreviations, full titles, and links to some WWW pages for a large variety of biological and medical journals (Lloyd Hough).

Emed alert setup

INTERNET & PUBLISHING
Manuscripts
HTML Help & Tools
Site Submission

FUNDING
Agencies funding

Areas

Department of Defense Funding

Department of Defense

 

 

Funded Researcher Databases

News Granting

NIH Road Map

NIH Road Map

|||New Pathways to Discovery

|||Research Teams of the Future

|||Re-Engineering the Clinical Research Enterprise

RFAs, PGAs etc.

NSF Funding

NSF Funding

 

Search

International Grant Finder

Writing Advice

CAREER For a more extensive set of links see: BioCareer@elegansNet
Announcements & Reports

Advice & Career Discussion

Advice & Career Discussion

Career Networks

Focus on Careers

  • Drug Discovery career & events (Science April 20, 01).
  • Proteomics - advantages in technologies and their use in drug discovery (Science April 13, 01)

Bulletin Boards

Job opportunities in:

Biotech/Pharma companies: Select from the list of a few companies actively recruiting below, or see a more complete list at SciJobs.org or at BioView (comprehensive biotechnology/pharmaceutical employment site with thousands of job listings in all disciplines .....)

Movers & Shakers

 

Search Firms and Employment Agencies

Relocation, Salary, Cost of living comparisons

Salaries and job satisfaction


ANATOMY; CELLS; PICTURES; PHOTOS; IMAGES; VIDEOS; CINEMA, & MOVIES.
C. elegans (elegans Cinema)

WormAtlas

Angler: A Browser of C. elegans Embryo Development In Time and Space - Sanger Center.

Slidable Worm SteinLab, CSHL.

EM Center (Center for C. elegans Anatomy).

Parts Index - Leon Avery's Server

Photos, pictures, images, movies, etc.

Virtual Embryo (Ed.: Leon Browder & Laurie Iten; Calgary U. & Purdue).


Go to C. elegans Databases

Fly Brain Atlas
Human
Mouse Whole mouse
Plants Anatomy & Glossary

Xenopus

Tadpole Movies

Amphibian development

Zebrafish

Developmental Atlas

 

COURSES STRICTLY
 
TEXTBOOKS, BOOKS, COURSES, GUIDES, etc.

  Bookshelf@NCBI

Biochemistry Biochemistry

Bioinformatics

Biology

Cells-Molecules-Organisms

Chemistry & Physics

 

Functional Genomics books

Genetics

Graphics & Presentation

Stanford Graphics

Medical Study Guides

Mendelian Genetic

Microscopy

Molecular Biology

Nucleic Acids Organisms

Proteins

Statistical Concepts

  • StatSoft - basic statistics, experimental design, linear regression, and much more.
TUTORIALS, FAQ, & GUIDES
Animations Tutorials

Biochemistry and Organic Chemistry (General,)

Bioinformatics tutorials

Biology & More

Biosciences - French sites (Infobiogen & Pasteur institute) cover the following areas and more:

  • Biochemistry
  • Bioinformatics
  • Biophysics
  • Chemistry
  • Microbiology
  • Neuroscience

Biochemistry

Bio-computing tutor

C. elegans tutorial

Cells-Molecules-Organisms

 

Chemistry tutorial

Chemoreception

Development

DNA Structure

 

FACS

Graphics & Presentation

     Stanford Graphics

Math

Mendelian Genetic

Microscopy - Cromey DW, U. Arizona

Molecular Biology

Neurobiology

Physics

Transgenic

 

DATABASES & TOOLS
Brief description of frequently used Tools & Service
Choose database access method optimal for your needs:

 

Databases & Tools listed alphabetically in each category
 
AmphibiaWeb
Anticancer agents
ATCC
Alt-Splicing Catalog
Apoptosis
BioMagResBank
A Repository for Data from NMR Spectroscopy on
Proteins, Peptides, and Nucleic Acids (Department of Biochemistry University of Wisconsin-Madison).
BBID-Biological Biochemical Image Database -
a searchable database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships. It is of use to those who are working with large sets of genes or proteins using cDNA arrays, functional genomics, or proteomics (Kevin G. Becker, NIA, NIH).
BLOCKS - Multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins.
Brain
  • Braininfo - Provides NeuroNames, Template Atlas of the Primate Brain, & NeuroMaps ( U. of Washington, U.S.)
  • Image database - (National Functional Magnetic Resonance Imaging (fMRI) Data Center)
Calcium binding proteins database (EF-hand). Provides tools, databases, and links on all aspects of calcium binding proteins (Melanie Nelson/Walter Chazinlab; The Scripps Research Institute; Structural Biology Program at Vanderbilt U).
Cancer DB

|||||Cancer

CarbBank - Complex Carbohydrate Structure Database (Scott Doubet).

C. elegans

C. elegans DB

|||||WormBase -SteinLab/CSHL

|||||NEMBASE -- A database resource currently being developed at B'NG to provide a simple easy-to-use access point to the publically available nematode sequence and functional data as part of our Expressed Sequence Tag (EST) sequencing initiative [john.parkinson@ed.ac.uk]

|||||TIGR C. elegans Gene Index (CeGI)

|||||BC cancer Agency

Chemoreception
CGC C. elegans Genetic Center

Chemistry

Chromosome 12 - Human/Sanger
Codon Usage (all organism)
COGs Phylogenetic classification of proteins encoded in complete genomes

Combinatorial Chemistry

Computational Bioscience

Conserved Diseases

CONTIGS
COS
CRISP
Crystallization db
Cultured Cell Bank
CYP450
Cytokine online pathfinder encyclopedia (COPPE; Horst Ibelgaufts at the Laboratory of Molecular Biology, Gene Center, University of Munich; LMU).
Cytomer
D. discoideum
Disease
  • MedGene database for assembling disease-gene citation matrices from over 11 million Medline records, with relationships normalized into rank order.
  • GeneDis Human Genetic Diseases Compare your sequence to a sequence present in GeneDis with Pairwise Alignment; compare your protein or DNA sequence to all protein or DNA sequences in GeneDis, with FastA; compare your protein sequence to DNA sequences present in GeneDis, with TFastA (Bioinformatics Unit Faculty of Life Science Tel-Aviv University
    Israel).
  • Disease & Orphan Drugs: (OrphaNet, Infobiogen, Cedex, France)
DNA sequences alignments can be done rapidly with SSAHA
DNA-Binding Proteins

DNA Microarrays

DNA Miropeats - discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically (jparsons, MRC, UK).

DNA Replication (Mark Griep; Center for Biotechnology, U. Nebraska-Lincoln).

Drugs

Elemental Data Index

EMBOSS suite of applications - containing around 100 programs; these are just some of the areas covered:

  • Sequence alignment
  • Rapid database searching with sequence patterns
  • Protein motif identification, including domain analysis
  • EST analysis
  • Nucleotide sequence pattern analysis, for example to identify CpG islands.
  • Simple and species-specific repeat identification
  • Codon usage analysis for small genomes
  • Rapid identification of sequence patterns in large scale sequence sets.
  • Presentation tools for publication
Endocrine Pancreas Consortium (EPConDB)
Enzyme - a nomenclature database, including searches by various methods and links to related databases (HMS Beagle 5/11/00).
e-PCR (all organism)
EST
  • est_genome - a software tool to aid the prediction of genes by sequence homology. The program will align a set of spliced nucleotide sequences (ESTs cDNAs or mRNAs) to an unspliced genomic DNA sequence, inserting introns of arbitrary length when needed. In addition, where feasible introns start and stop at the splice consensus dinucleotides GT and AG (HGMP,MRC,UK)
Ethanol db
FingerPRINTScan

FishBase

Flavor & Fragrance
FLY
Funded Research
Fungus2000 db - British Microbiological Society
GABA Agent
GDB
Gene Exp & Function (C. elegans)

Gene-finding software Site

Read about it

  • ACEMBLY - A graphic interactive program to support shotgun and directed sequencing projects (Danielle & Jean Thierry-Mieg and Ulrich Sauvage, CNRS-CRBM, Montpellier, France).

  • Genome annotation database for vertebrates (VEGA).

  • BLOCKS

  • est_genome - a software tool to aid the prediction of genes by sequence homology. (HGMP,MRC,UK)

  • FGNEH

  • Fgenes+

  • GENEID

  • GENIE

  • GENSCAN

  • GeneMarkHMM

  • GRAIL

  • GlimmerM

  • GeneBuilder

  • Genemark (The Borodovsky Group
    School of Biology,
    Georgia Institute of Technology).

  • HMMGene

  • MORGAN - an integrated system for finding genes in vertebrate DNA sequences. MORGAN uses a variety of techniques to accomplish this task, the most distinctive of which is a decision tree classifier (S. Salzberg, A. Delcher, K. Fasman, and J. Henderson. A Decision Tree System for Finding Genes in DNA).

  • SIM4 - addresses the problem of efficiently aligning a transcribed and spliced DNA sequence (mRNA, EST) with a genomic sequence containing that gene, allowing for introns in the genomic sequence (taking into account consensus splice signals) and a relatively small number of sequencing errors (Florea et al. 1998, Genome Res. 1998 8:967-74).

  • VEIL - the Viterbi Exon-Intron Locator uses a custom- designed hidden Markov model (HMM) to find genes in eukaryotic DNA (John Henderson, Steven Salzberg, and Ken Fasman at Johns Hopkins University).

  • Wise2/Genewise

Gene Annotation Tools

Gene Annotation sites

Gene Annotation Tools

  • Bioxml

  • BostonAnnotator - Simultaneous analysis of genomic sequence using BLASTx and BLASTn homology searches and the GENSCAN protein prediction program. The results are displayed graphically in a manner such that alignments for all searches appear in the same window, allowing the rapid assessment of which positives correspond to real genes (Beier and Yang, Harvard U., U.S.)

  • GFF

  • GFFTOOLS

  • Publications

Gene Resume

  • euGenes (Eukaryotic Genes db; Indiana, USA).

  • Entrez All Genomes (NCBI).

  • GeneCards (human + disease; Weizmann Institute, Israel).

  • Gold (Integrated Genomics Inc., Chicago, IL, USA). |||||Genomic links (Gold).

  • KEGG: Kyoto Encyclopedia of Genes and Genomes - providing metabolic & regulatory pathways of unicellular and mutlicellular organisms (Institute for Chemical Research, Kyoto U.).

  • Stress Genes & their protein products Network - European Science Foundation (Maresca, Italy; Mayer, U.K.).

  • TIGR (Institute for Genome Research, Rockville, MD, USA).

Genes
Gene Trap Insertions

Genetic code

Genetics
Genetics & Genomics

Gene Knockout

Genome Shotgun Reads
Genomic CONTIGS
GOLD - (Genomes On Line db) providing access to all genome db, indices, etc.
Glycolysis
G Protein Coupled Receptors (GPRC)
Stem Cell Database
HGBASE - HGBASE Curated and annotated sequence variations in the human genome are presented with details of how they are physically and functionally related to the closest neighboring gene. Records include SNPs, Indels, simple tandem repeats, and other sequence alternatives [Karolinska Institute (Sweden), European Bioinformatics Institute (UK), European Molecular Biology Laboratory (Germany), & Interactiva GmbH (Germany) hosting a parallel HGBASE Web site with genotyping products (Science May 2000).
Histone Sequence
HIV -
HMMER 2.1.1
Profile hidden Markov models for biological sequence analysis - can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis (Wash U., Stl.)
HMMFS - search for repeats (S. Eddy & R. Durbin; Institut Pasteur, france).

Homeobox genes

HotMolecbase targets for drugs

Human - Mouse

Hybridoma Bank
Immunology
InterPro protein domains & functional sites

Intron Database

Ion Channels:

KEGG: Kyoto Encyclopedia of Genes and Genomes - providing metabolic & regulatory pathways of unicellular and mutlicellular organisms (Institute for Chemical Research, Kyoto U.).
LocusLink? - curated sequences, description & alphabetic lists of genetic loci, search function, , related links, etc. (NCBI, USA).
Metabolic & regulatory pathways - KEGG: Kyoto Encyclopedia of Genes and Genomes - providing metabolic & regulatory pathways of unicellular and mutlicellular organisms (Institute for Chemical Research, Kyoto U.).

Microarrays

Microbial db

Model Organisms

Projects & Databases

Molecular Probe human/ viral (MPDB)

Monosaccharides
Mouse
Muscle
Mutation db - HUGO Mutation Database Initiative (compiled by Horaitis R, at the Genomic Disorders Research Centre, Melbourne. Report errors, changes or additions, including "dead" sites).

Human Gene Mutation Database (Institute of Medical Genetics in Cardiff., U. of Wales College of Medicine).

VMD2 Mutation Database- mutations and polymorphisms in the VMD2 gene, U.sity of Wuerzburg, Germany

 

Nematodes
Neurospora
NEXTDB - nematode expression pattern database
NMR
  • BioMagResBank
    A Repository for Data from NMR Spectroscopy on
    Proteins, Peptides, and Nucleic Acids (Department of Biochemistry University of Wisconsin-Madison).
Nuclear Receptors
Organelle Genome
  • GOBASE - taxonomically broad, organizes and integrates diverse data related to organelles & especially to mitochondria.

Oligonucleotides human/viral

(MPDB)

ORNL

OWL -nonredundant protein

sequence with links to other db

Pancreas
  • Endocrine Pancreas Consortium (EPConDB)
Pathways
  • Dicussion of Complex Biological Pathways
  • BBID-Biological Biochemical Image Database -
    a searchable database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships. It is of use to those who are working with large sets of genes or proteins using cDNA arrays, functional genomics, or proteomics (Kevin G. Becker, NIA, NIH).
  • BIND - Biomolecular Interaction Network Database
  • Boehringer Mannheim Pathways Chart
  • BRITE - Cell Cycle & Development
  • CSNDB - Cell Signaling Networks Database of signaling pathways of human cells constructed on ACEDB and inference engine CLIPS , and has a linkage to TRANSFAC. [Takako Takai-Igarashi and Tsuguchika Kaminuma; National Institute of Health Sciences (NIHS)].
  • DIP - Database of Interacting Proteins
  • EcoCyc - Encyclopedia of E. coli Genes and Metabolism
  • Interactive Fly
  • KEGG: Kyoto Encyclopedia of Genes and Genomes - providing metabolic & regulatory pathways of unicellular and mutlicellular organisms (Institute for Chemical Research, Kyoto U.).
  • Kohn Molecular Interaction Maps
  • Nuclear Receptor Resources
  • PathWays+ Metabolic Database
    (Raymond S. Ochs
    Veejay K. Sani;
    St. John's University).
  • STKE - Signal Transduction Knowledge Environment.
  • STKE db & model organisms

  • WIT - a www-based system to supporting curation of function assignments made to genes and the development of metabolic models (Argonne Computational Biology Group).

Parasites
Pedant - a protein extraction, description, and analysis tool. Supplies computational analysis of sequences, genome analysis and annotation, and information on unfinished sequences (HMS Beagle; 5/12/00).
Phenology Model
Physics
PhysioNet - physiologic signals and related open-source software
Primase

PRINTS

PROMISE - The Prosthetic groups and Metal Ions in Protein Active Sites Database Version 2.0 (U. of Leeds).
Protein MSPcrunch: A BLAST post-processing filter - searches SWIR (non-redundant data bases of SwisProt, SP-TREMBL, & WormPep)(Sonnhammer &, Durbin).

Protein Data Bank - single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.

Protein Kinases

Proteome Analysis
PSORT - Protein Cellular localization sites in Cells
Puffer Fish
Rat Databases
Rat Genomic Tools
Repeatmasker
 Restriction
Retroviruses
RNA (Scottish RNA Club; MRC, UK).
  • Non-coding
  • Ribosomal Database Project (RDP) provides ribosome related data services including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences
  • RNA Editing - Larry Simpson (UCLA, USA).
  • RNA Modification - Crain & McCloskey (Chem. & Biochem, U. Utah, USA).
  • RNA World - (IMB Jena, Germany).
  • rRNA - Biochemistry: Molecular Biology (U. Antwerp (UIA), Belgium).
  • Small RNA - a searchable database (K. Perumal, J. Gu, Y. Chen, R. Reddy;
    Baylor College of Medicine).
  • Small RNA in model Organisms (K. Perumal, J. Gu, Y. Chen, R. Reddy;
    Baylor College of Medicine).
  • snoRNA - Sean Eddy Lab (Genetics, Wash. U. St. Louis, MO, USA).
  • tRNA - Stephan Brock, Laboratorium für Biochemie (Bayreuth, Germany).
  • TRNAscan_SE - Search for tRNA (S. Eddy, Wash. U., StL.).
RNAi
Sanger Center Sitemap
SCOP Structural Classification of Proteins

SNPs

Sequencing Centers

Signal Transduction - CSNDB
Signal Transduction Pathways
S/MAR transaction

SRS6-EBI A unified db

 SSAHA aligns DNA sequences rapidly.
Sterols
Stress Genes & their protein products Network - European Science Foundation (Maresca, Italy; Mayer, U.K.)
STS electronic PCR
SWISS-PROT nonredundant,
annotated protein sequences

TAB: Human/viral

oligonucleotides up to

100-bp (MPDB)

Taxonomy Browser

Taxonomy (comparative) - includes some 200,000 species of plants, fungi, animals, bacteria, and protists

TCA Cycle

Transcription Factor

Transgenic Mutation db
TrEMBL
Computer-annotated supplement to SWISS-PROT
VAST - Searches for similarity between proteins

Vectors

Virology
WormBase
Worm db links
Xenopus
Yeast
Zebrafish

Integrated Databases &

Informatics Tools - Meaning and level of "integration" differs considerably at sites below:

  • SeWeR - a single door to all the common web- based services for sequence analysis. A highly promising site with some of the features of Celera site which we have liked. Any one with interest in sequence analysis should visit, use, and watch its development (elegansNet review 6/19/00)(Malay K Basu; Centre for Cellular and Mol. Biol., Hyderabad, India).
  • 3DinSight an integrated database and search tool for structure, property and function of biomolecules (BioInfo Bank).
  • EBI - European Bioinformatics Institute (EBI) is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures (UK).
  • EMBL DNA database
  • Additional sequence search and data retrieval tools
EMBL computational services:

|||||Sequence

||||Structure

|||||Information Services

AG Bioinformatics - focuses on regulatory genomic signals and regions, in particular those that govern transcriptional control. GBF develops database and software tools for identification of sequence elements and their context in newly unraveled genomic sequences (Germany).

|||||Databases:

The TRANSFAC database Release 4.0!
TRANSPATH Gene- regulatory pathways.
CYTOMER Physio. systems, organs and cell types.
S/MARt DB Information about scaffold/matrix attached regions and the nuclear matrix proteins involved in the interaction with nuclear matrix. From yeast to human.

|||||Tools - Sequence Analysis: Search for transcription factor binding sites in your own sequences and more ...

NCBI - National center for Biotechnology Information; NIH; NLM).

||||||Databases & Informatics

Entrez All Genomes

GenBank

Molecular databases

Literature databases

Genomic biology

Tools for data mining

Tutorials

FTP site

Hot Spots

Cancer genome anatomy project

Clusters of orthologous groups

Coffee Break

Electronic PCR

Genes and disease

Human genome resources

Human/mouse homology maps

LocusLink

Malaria genetics & genomics

ORF finder

Reference sequence project

Retrovirus resources

Serial analysis of gene expression

UniGene

VecScreen

DATABASES - Category List (includes description of tools - Nucleic Acids Research 2002 Database Issue of Nucleic Acids Research

Access database based on what you have and what do you want to do with it?

Got a Clone:

Compare

Briggsae & elegans

Got a disease (or a gene) and want to see associated genes (diseases) - MedGene

Got Name:

Get Sequence

NetEntrez

ORNL

SRS

Get Much Info.

Got X: Get Worm DNA

Got a Sequence:

Analyze it at one site via:

  • SeWeR - a single door to all the common web- based services for sequence analysis. A highly promising site with some of the features of Celera site which we have liked. Any one with interest in sequence analysis should visit, use, and watch its development (elegansNet review 6/19/00)(Malay K Basu; Centre for Cellular and Mol. Biol., Hyderabad, India).

  • Imagene 3.1 - providing an improved display interface for a more clear distinction between known genes, candidate gene clusters and candidate gene contigs (I.M.A.G.E. Consortium)

  • Online Analysis Tools (Kropinski, Ontario).

  • est_genome - a software tool to aid the prediction of genes by sequence homology. The program will align a set of spliced nucleotide sequences (ESTs cDNAs or mRNAs) to an unspliced genomic DNA sequence, inserting introns of arbitrary length when needed. In addition, where feasible introns start and stop at the splice consensus dinucleotides GT and AG (HGMP,MRC,UK).

  • EMBOSS suite of applications - a new, free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community (read more in CCP11 News, 8/11/00). Within EMBOSS you will find around 100 programs (applications). These are just some of the areas covered:

    • Sequence alignment
    • Rapid database searching with sequence patterns
    • Protein motif identification, including domain analysis
    • EST analysis
    • Nucleotide sequence pattern analysis, for example to identify CpG islands.
    • Simple and species-specific repeat identification
    • Codon usage analysis for small genomes
    • Rapid identification of sequence patterns in large scale sequence sets.
    • Presentation tools for publication
    • And much more.

Got a Family Sequence Concensus:

  • HMMER 2.1.1
    Profile hidden Markov models for biological sequence analysis - can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis (Wash U., Stl.)

Name?

Blast:

Blast to SNP maps
Cancer Gene?

Common Structure?

TRADAT

CONTIGS

Human

Mouse (Wash. U.)

Genome Channel ORNL

Cross-Reference Human

& Yeast Genes

HGBASE - HGBASE - HGBASE Curated and annotated sequence variations in the human genome are presented with details of how they are physically and functionally related to the closest neighboring gene. Records include SNPs, Indels, simple tandem repeats, and other sequence alternatives. Records are [Karolinska Institute (Sweden), European Bioinformatics Institute (UK), European Molecular Biology Laboratory (Germany), & Interactiva GmbH (Germany) hosting a parallel HGBASE Web site with genotyping products (Science May 00).

Encodes?

BCM Launcher

GRAIL

GeneFinder

Gene Browser

Intronerator

Mandelian Inherit..

NCSA

ORNL

Sanger Center

TRADAT

UniGene

Expression?

Array Links

C. elegans

EBI - Robinson

I.M.A.G.E.

Kim Lab

Spotted cDNA

Rockefeller - Li

SAGE

Function? WIT

Fold RNA or DNA
Includes Vec. Seq?

Knockout Gene

C. elegans Consortium

Mouse:

db

Service

LocusLink? - curated sequences, description & alphabetic lists of genetic loci, search function, , related links, etc. (NCBI, USA).

Mask Repeats?

REPEATMASKER

Motif & Domain Search

FingerPRINTScan

PatternFind

pfam

PRINTS

Prosite

SMART

VAST - Searches for

similarity between

proteins

Molecular Modeling

New Discovery?

PubMed

Oligos & Primers

Oligo design

PrimeMate

Primer Finder

ORF: Compare Find

Organization?

Alt-Splicing Catalog

CBS Prediction Server

Intron Database

Intronerator

TRADAT

Pathways?

Phylogenetic lineage?

COGnitor?

Print/Shade multiple Alignment:

BOXSHADE

Protein-DNA Align

CLUSTALW

Protein:

All organism

informatics tools

Pedant - a protein

extraction,

description, and

analysis tool.

Supplies

computational

analysis of sequences,

genome analysis and

annotation, and

information on

unfinished sequences

(HMS Beagle; 5/12/00).

Analyze Seq. NPS@

Classify your protein

sequence - ProtoMap

provides an automatic

hierarchical

classification of all

protein sequences in

the SWISSPROT and

TrEMBL databases

(Stanford U.)

Conformation

Conserved Ungapped

Segments? BLOCKS

Drug Target?

Fold, Move, Align, etc.

Metal ions?

PROMISE - Metal

Ions in

Protein Active Sites

database (U. Leeds).

Phylogenetic Lineage?

COGs

Prosthetic groups?

PROMISE - The

Prosthetic groups

in Protein Active

Sites (U. Leeds).

 

Similarity to other

Proteins?

BLOCKS;

SWISS-PROT &

TrEMBL; VAST

Motif & Functional

Sites?

FingerPRINTScan

InterPro

PatternFind

pfam

PRINTS

Prosite

SMART

TMHMM (v. 2.0) -Prediction of transmembranehelices in proteins

VAST - Searches for

similarity between

proteins

Sorting Signals?

Structure/F Predict?

OCA

Structural

Classification?

SCOP

Submit to Banks

C. elegans - CGC

Fly

Human

Mouse

Xenopus

Zebrafish

Transcription Factor

Binding Sites?

FunSiteP

MatInspector

PatSearch

TRADAT

 

View Structure

WebMol

Got Retrovirus: Get tools for

Got Results: Significant?

Stat. Tools & More

LABS, GROUPS,

RESEARCHERS

Academic Labs
C. elegans
Drosophila
Saccharomyces
Commercial Labs

C. elegans

Communities (C. elegans)
Researchers Profiles

C. elegans

 

MATERIAL
C. elegans material

Mouse Material

Material applicable to More than one organisms

Banks material

  • Cell Analysis & Modeling Provides software tools for modeling cell physiological processes. Presented as Java applets, the tools are free to academic users (The National Resource for Cell Analysis and Modeling, NRCAM).
    • calcium waves sweeping across a neuron
    • mitochondrial respiration
    • nuclear envelope disintegration
Chromatin & Nucleus
  • Cellnuleus.com provides

Antibody Database Descriptions and labeling for antibodies to nuclear proteins

Methods Sites containing information on related methodology

Microscopy Information on microscopy and live cell imaging

Fluorescent Proteins Useful information on the use of fluorescent proteins

Image Analysis Links to quality shareware and information on image analysis

Equipment Links to quality equipment for microscopy and cellular imaging

Sorting methods
  • Introductory - Geoff Osborne site
  • Compensation - Discussion & Quiz - Mario Roederer; NIAID, NIH

  • Flow Cytometry - links list at the Salk Institute, La Jolla, CA, U.S.)
  • "COPAS" = "Complex Organism Parametric Analysis and Sorting. Products automating the high-speed preparation and analysis of organisms, such as the nematode C. elegans and the larvae of the fruit fly D. melanogaster (Union Biometrica).
GFP

Bioluminescence

Oligoribonucleotides (Xeragon)

Software Collections:

Bioinformatics

C. elegans

Collaboratory Tools:

  • Structural Biology

    • BioCoRE (Theoratical Biophysics Group, Urbana, Illinois, USA).

Gene Chip

  • CAGED (Cluster Analysis of Gene Expression Dynamics) is a program for the analysis of temporal profiles of gene expression data. To learn more, please enter here (Marco Ramoni, Harvard).

Genamics

Gene-finding software

  • ACEMBLY - A graphic interactive program to support shotgun and directed sequencing projects (Danielle & Jean Thierry-Mieg and Ulrich Sauvage, CNRS-CRBM, Montpellier, France).

  • BLOCKS

  • FGNEH

  • EMBOSS suite of applications - a new, free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community (read more in CCP11 News, 8/11/00). Within EMBOSS you will find around 100 programs (applications). These are just some of the areas covered:

    • Sequence alignment
    • Rapid database searching with sequence patterns
    • Protein motif identification, including domain analysis
    • EST analysis
    • Nucleotide sequence pattern analysis, for example to identify CpG islands.
    • Simple and species-specific repeat identification
    • Codon usage analysis for small genomes
    • Rapid identification of sequence patterns in large scale sequence sets.
    • Presentation tools for publication
    • And much more.
  • Fgenes+

  • GENEID

  • GENIE

  • GENSCAN

  • GeneMarkHMM

  • GRAIL

  • GlimmerM

  • GeneBuilder

  • Genemark (The Borodovsky Group
    School of Biology,
    Georgia Institute of Technology).

  • HMMGene

  • MORGAN - an integrated system for finding genes in vertebrate DNA sequences. MORGAN uses a variety of techniques to accomplish this task, the most distinctive of which is a decision tree classifier (S. Salzberg, A. Delcher, K. Fasman, and J. Henderson. A Decision Tree System for Finding Genes in DNA).

  • SIM4 - addresses the problem of efficiently aligning a transcribed and spliced DNA sequence (mRNA, EST) with a genomic sequence containing that gene, allowing for introns in the genomic sequence (taking into account consensus splice signals) and a relatively small number of sequencing errors (Florea et al. 1998, Genome Res. 1998 8:967-74).

  • VEIL - the Viterbi Exon-Intron Locator uses a custom- designed hidden Markov model (HMM) to find genes in eukaryotic DNA (John Henderson, Steven Salzberg, and Ken Fasman at Johns Hopkins University).

  • Wise2/Genewise

Gene Annotation-related

sites

Gene Annotation Format & Tools

  • Bioxml

  • BostonAnnotator - Simultaneous analysis of genomic sequence using BLASTx and BLASTn homology searches and the GENSCAN protein prediction program. The results are displayed graphically in a manner such that alignments for all searches appear in the same window, allowing the rapid assessment of which positives correspond to real genes (Beier and Yang, Harvard U., U.S.)

  • GFF

  • GFFTOOLS

Model Organisms

Projects & Databases

Gnutella - a software tool

that can bypass Internet

service providers and

allow computer users to

communicate directly

among themselves.

Statistical Analysis

access to many stat sites

offering online analysis

and tutorials (John C.

Pezzullo).

  • Statistical Applets - provides basic online stat analysis (McGraw Hill - Vadum Rankin).

  • Sample Comparisons: t-Tests, ANOVAs, Non-parametric Comparisons (John C. Pezzullo).

  • StatSoft - covers basic statistics, experimental design, linear regression, and much more (HMS Beagle 4/12/00).

  • StatView - Commercial site for downloading demo and purchasing StatView.

  • VassarStats - basic statistical number- crunching & procedure (Richard Lowry; Vassar College, NY, USA) (Science review 5.26.00:"Lowry strives to demystify the "magic rituals" behind the process."

Two-Hybrid & Three-Hybrid Systems

Vectors - Mal - all orgs

    


  • Kits - Transfection
    • GenePORTER - polyvalent, cationic lipids Genetherapysystems
    • Polyplus-transfection reagents designed for hepatocytes, macrophages & dendritic cell, epithelial & endothelial, and for tracking delivery with fluorescent tags.
    • Flip-In system For Generating Stable Mammalian Expression Cell Lines by Flp Recombinase-Mediated Integration. pdf
VIEWERS
  • Apollo Genome Browser - (Berkeley Drosophila Genome Project & Ensembl)

  • IUMSC - Examine a high-resolution model of many common chemicals and/or your favorite molecule (Indiana University Molecular Structure Center)

  • MMTK - The Molecular Modelling Toolkit - Providing an Open Source program library for molecular simulation applications [Hinsen K, Centre de Biophysique Moléculaire (CNRS), France]

  • NAMD - a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems; distributed free of charge and includes source code (Theoretical Biophysics Group, Beckman Institute, U. Illinois, USA).

  • Protein Explorer - a RasMol-like interface implemented in Chime offering greater assistance and automation; visual exploration of protein structure & protein:DNA interactions are made easier & more convenient than RasMol; Need Netscape 4 or later. (Claude Aflalo, Ben Gurion U.; Beer Sheva,Israel; BNS June 2000).

  • VMD - a freely available Visual Molecular Dynamics program that currently runs on both windows and Unix (Theoretical Biophysics Group, Beckman Institute, U. Illinois, USA).

  • Webmolecules - View your favorite molecule form db of 21,000 (Molecular Arts Corp.).

  • WebMol - display and analyze structural information contained in the Brookhaven Protein Data Bank (PDB); run as an applet or as a stand- alone application (Dirk Walther).

VENDORS, SAFETY, & SPECIALTY ITEMS

Suppliers - Antibodies

 

C. elegans work

Buy/sell used/new equip.

Read lab product reviews

Specialty Items

Portals

MICROARRAY DIRECTORY

MAD@elegansNet

All aspects via Ecole Normale Superieure (B. Martin & P. Marc; Paris, France).

ProteomicsSURF - A proteomics directory of  methods & protocols for novice and advanced users. Also included are links to Bioinformatics, Genomics, Microarrays, PCR, Crystallography, NMR, & Chromatography.

Data microarrays

  Human:

     Mouse

     Nematode

     Yeast:

 

DatDatabases Microarray

Databases (Ecole Normale Superieure) or mouse mammary db as listed below [LECB,NCI/FCRDC)]:

Data, mining, processing, & probe design

  • Standards at last!

     
  • CAGED (Cluster Analysis of Gene Expression Dynamics) is a program for the analysis of temporal profiles of gene expression data. To learn more, please enter here (Marco Ramoni, Harvard).
  • Array Designer - Helps by automating the selections of appropriate oligonucleotide probes or cDNA primer pairs for microarray analysis (Reviewed by S. Lalitha , BioMedNet May 11, 2001 · Issue 102).
  • MGAP - MicroArray Explorer - an exploratory data analysis facility for cDNA microarrays from mouse mammary tissue and databases from the Mammary Genome Anatomy Project (MGAP). A new enhanced version is available for download. This Java application works on Windows 95/98/NT, Macintosh, Solaris, Linux, and other Unix and Java enabled computers; Tutorials
    [LECB,NCI/FCRDC)].
  • CLEAVER : "The Cleaver (Classification of Expression Array Version 1.0) internet site providing tools for analysis of microarray expression data including visualization, classification, and clustering. Computations are done on the server side & taking take no longer than five to ten minutes to compute" (Snowdeal.org, 7/1/00); read about it here (Stanford Biomedical Informatics).
  • Many other Data processing links (Ecole Normale Superieure (B. Martin & P. Marc; Paris, France).

Data Standard

Standards at last!

Innovations reverse transfection micro arrays

Microarray data - Protein function & biochemical Network (European Bioinformatics Institute).

Human:

Mouse

Nematode

  • SAGE
  • C. elegans - how to prepare samples for submission to Kim's Lab for microarray analysis

Yeast:

Special Microarray Links

PROTOCOLS
Cell Culture methods
Innovations cell culture

Resource Centers CC

C. elegans Protocols

All Organism Protocol Collections

Banks:


Bioluminescence

Buffers, Calculations, PH etc.

Cancer Gene How to? The Cancer Genome Anatomy Project (CGAP) - NCI

Cell Analysis & Modeling Provides software tools for modeling cell physiological processes. Presented as Java applets, the tools are free to academic users (The National Resource for Cell Analysis and Modeling, NRCAM).

  • calcium waves sweeping across a neuron
  • mitochondrial respiration
  • nuclear envelope disintegration

Cell Structure - A Web Atlas of Cellular Structures Using Light and Confocal Microscopy (Sheela Konda, Steve Rogers, and Daniel E. Weber; University of Illinois at Urbana-Champaign).
 Molecular Cloning ethods

Molecular Cloning

Flow Cytometry & Sorting

  • "COPAS" = "Complex Organism Parametric Analysis and Sorting. Products automating the high-speed preparation and analysis of organisms, such as the nematode C. elegans and the larvae of the fruit fly D. melanogaster (Union Biometrica). Automated Sorting & Analysis of C. elegans

Gene Expression Material

GFP & Bioluminescence

Graphics & Presentation

Stanford Graphics

Measurement Converter

Methods in the News

Microscopy Microscopy

PCR Protocols

Phage display PDisplay

RNA Protocols

SNP: Mut. detection SNP

Statistics

Statistical Applets - access to many sites offering online analysis and tutorials.

  • Statistical Applets - provides basic online stat analysis (McGraw Hill - Vadum Rankin).

  • Sample Comparisons: t-Tests, ANOVAs, Non-parametric Comparisons (John C. Pezzullo).

  • StatSoft - covers basic statistics, experimental design, linear regression, and much more (HMS Beagle 4/12/00).

  • StatView - Commercial site for downloading demo and purchasing StatView.

  • VassarStats - basic statistical number- crunching & procedure (Richard Lowry; Vassar College, NY, USA) (Science review 5.26.00:"Lowry strives to demystify the "magic rituals" behind the process."

Transfection

Transfection methods

Two-hybrid & Three-hybrid

  • Brief Overview
  • A review of two & three hybrid system in March 2001 issue of BioTechniques (Serebriiskii et al.)
  • Yeast Two-Hybrid: State of the Art - a review of the technology; includes text, graphics, & PDF version (Van Criekinge1 & Beyaert; Belgium; 1999/2000?).
  • Finding a Mate - Two-hybrid systems ease detection of protein-protein interactions (Cunningham BA, Scientist 15[7]:26, Apr. 2, 2001)

  • Labs:

    Roger Brent - protocols and application of interaction trap

    Stan Feilds - protocols and interesting applications

    Marv Wickens - three-hybrid system for detection of RNA-protein interactions and pdf files describing & reviewing the method.

  • large-scale (Walhout et al. kim).

  • Two-hybrid libraries from many sources including yeast, c. elegans, fly, mouse, rat, and human (Origene).


REFERENCE SHELF

Dictionaries refshelf


Atlas & Encyclopedia

Catalogues

  • Islamic Medical Manuscripts - "inspired by Hippocrates, Galen, and other Greek and Roman predecessors, made extensive efforts to understand the remarkably wide range of diseases they faced ..............." (New: 6.6.00; National Library of Medicine, USA).

Calculators

Calculators, Converters & Tables

|||||||Chemistry Web Book

Easily searchable (NIST)

||||||||Currency Converter

||||||||Dilution Calculator

||||||||||Financial Calculators

|||||||||Science Tables

||||||||Measurements

||||||||Oligo Calculator

|||||||Periodic Tables

|||||||Physical Reference Data

physical constants,

atomic spectra

|||||||TM Calculator for oligo

Directories/Guides/Indices

||||||||Biology

|||||||||Bio- & Cheminformatics

  • elegansNet - The search site for identifying resources in biochemical, molecular, cellular, system, and organism biology, including over 25,000 indexed links, accumulated since 2000, from topic menus or from search interface.

  • Research Informatics Consult Service - a portal to organism data bases (Eskind library of Vanderbilt U).

|||||||||Biology, Biochemistry &

Molecular Biology

|||||||||Biophysics

|||||||||Biotechnology

  • BioWeb - a collection of biological resources. Covers botany, ecology, genetics, introductory biology, and much more (BioMedNet 4/24/00).

  • elegansNet - The search site for identifying resources in biochemical, molecular, cellular, system, and organism biology, including over 25,000 indexed links, accumulated since 2000, from topic menus or from search interface.

||||||||Chemistry

||||||||Chromatin Network

||||||||Development

|||||||Genetic

|||||||Immunology

|||||||Microbiology & Virology

|||||||Neuroscience

|||||||Pharmacology

|||||||Physiology

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Associations

Associations, Institutes, laboratories, organizations, foundations ...

Search for:

Bioinformatics Institutes -

(U. Düsseldorf).

Selected few

Manuals

Molecular Viewers
  • Protein Explorer - a RasMol-like interface implemented in Chime offering greater assistance and automation; visual exploration of protein structure & protein:DNA interactions are made easier & more convenient than RasMol; Need Netscape 4 or later. (Claude Aflalo, Ben Gurion U.; Beer Sheva,Israel; BNS June 2000).

  • Webmolecules - View your favorite molecule form db of 21,000 (Molecular Arts Corp.).

  • WebMol - display and analyze structural information contained in the Brookhaven Protein Data Bank (PDB); run as an applet or as a stand- alone application (Dirk Walther).

Quotation

Publishers & Book Sellers

Societies refere

BIOTECH - PHARMA
All Purpose
Advanced Technology Program (ATP) - NIST - National Institute of Standards and Technology - Technology Administration, U.S. Department of Commerce
Biotechnology regional index
  • Ireland - BioResearch Ireland (The Hubsite for five campus-based research centres of Irish Biotechnology).
Buyers Guide & Exhibits
  • TechExpo - an exhibition of high technology. Supplies a buyer's guide, company information, newsletters, and more (HMS Beagle 4/10/00).
Clinical Trials
  • Biotechnology Nexus - Supplies clinical trial updates, information on companies, feature articles, news, and other resources (HMS Beagle 4/12/00).
Clubs
DNA Vaccine biotech

ABC DNAVAC

Commercial Labs DNAVEC

Labs DNAVAC

Publications DNA

Resource Centers DNAvac

  Safety - DNA vaccines

       Genome-integration

       Factor-competition

Vector design, Construction, Quality Control, & Delivery

Searches DNAVEC

  • EpiVax - Screen any of 40,000 published protein sequences of the chameleon-like HIV-1 virus, including tens of thousands of sequences from HIV-1 strains afflicting African and Indian populations, for putative epitopes (EpiVax & Brown U., Rhode Island, U.S.).
  • HIV Protease Structural Database

DrugDiscovery

Drug Discovery -

DDD@elegansNet

Audio & Video

Consortiums drug dis.

  • HIP - Harvard Institute of Proteomics.

Drug Development scheme

Gene Therapysites

Gene-Therapy Sites & ResourcesGeneT

Journals & Zines

rug disc Meeting & Conferences

Meetings & Conferences

Outsourcing Pharmaceutical Development and Discovery Portal

Pharmacogenomics

Publications & Books

Societies sdd Socdd

Two-Hybrid System

US Gov. Initiatives

 

Virology -vaccines

Vendorsdd biotech

 

Ethical & Legal
  • Astrolabe - an ethical examination of virtual technologies. Includes background information, discussions on a variety of topics, and an online journal (HMS Beagle 4/11/00).
  • Bad Patents - legal resources and tools. Includes articles, information on biotechnology patents, a newsletter, and related sites (HMS Beagle).
  • ELSI Project - Ethical, legal, and social issues in science. Includes articles on air pollution, genetic patents, sustainable development, and other topics.
HIGH-MEDIUM DENSITY/THROUGHPUT SCREENING (HTS/HDS)
Assays

   Fluorescent Microscope-based

    Transfected Cell Microarrays

    GFP/xFP

    Other Assays

   Conferences & Meetings HTS

  • IBC's ScreenTech Conference
    March 12-16, 2001 · San Diego, CA
    • Compound Handling, ..
    • Cell Lines for Productive HTS
    • Virtual Screening and Data Mining ..
    • Project Management..

   Journals

   Reports HTS

   Vendors & Services HTS

News, Jobs, & More
Pharmacogenomics
Resources Information

MEDICINE/HEALTH
Alternative & New Medicine
Clinical Trials med
 

More disease

Disease search from alphabetical lists:

  • American Lung Ass.

  • GENEClinics - Summaries of some 70 disorders, (Alzheimer's Wilson's disease, etc.). Reviews include diagnostic info and links to genome databases; a related site lists genetic testing labs. Science 288, 7 April 2000.

  • Karolinska Institutet (Stockholm, Sweden)

  • NCBI (National Institute of Biotechnology Information).

  • PathWeb - includes a search tool that combs pathology image archives across the entire Web (Science April 21, 00).

  • PEDBASE (Pediatrics, Vanderbilt U.)

Disease (Selected List)
Alzheimer
Asthma
  • Breath of Life - History of asthma including research information, famous people who had asthma, and related links (HMS Beagle 3/13/00).
Attention Deficit Hyperactivity Disorder - Symptoms of ADHD, treatment information, and more. From the NIMH (HMS Beagle 4/12/00).
Algae related illness
Atherosclerosis
Cancer

 

Diabetes

Huntington (Smith et al.)

Infectious disease

Inherited Disease

Literature 1; 2

Mad Cow

Neuromuscular

Parkinson

Respiratory

Werner Syndrome

Disease gene conservation

Disease Models

C. elegans

Mouse

Drug Stores

Epidemiological
  • Emerging Infections Information Network - Supplies disease information, a forum, and related links HMS Beagle 4/11/00).
  • FoodNet - supplies information on food-borne diseases, epidemiological studies, related links, and more. From the Centers for Disease Control and Prevention (HMS Beagle 4/11/00) .
Ethical/Social
  • ELSI Project - Ethical, legal, and social issues in science. Includes articles on air pollution, genetic patents, sustainable development, and other topics.

Gene Resume

  • GeneCards (human + disease).

  • HGBASE - Summarizing known sequence variations in the human genome (Science 5/00).

Genetic Counseling -