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Genome Browsers-Gene Resume,
 Data Mining, Gene-finding-Tools,
Annotation Publicaion-Database-Help,
 Ontologies
DNA-Repeats-Introns-Defense,
Haplotypes, SNP,
 Genome/Evolution, Omes
    WebQTL: Cis-Elements
Gene Expression-Gene Trap/
 Gene Targeting, Mutagenesis,
L1 Retrotransposon, KnockOuts/
KnockIns, DNA-shuffling-
Compare, Phenotypes

RNA & RNAi

Proteome; Interactomes; HDS/HTS; GFP/xFP

Arrays: DNA; Protein-Membrane;

Small molecule; Frozen Cell;

 Transfected Cell

Collaborate; Courses; Textbooks

Tutorials-Animation-FAQ-Guides;
Development Cinema; elegans
Cinema; Pathways Pictured

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

Anisotropy
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
Fluorescence anisotropy Fluorescence anisotropy microplate assay (FAMA)
FRET Gene Gun
Gene KO Genetic Code
Gene Silencing Gene Therapy
Gene Trap
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
PCR-SOE
Proteomics Protein  Chips
Protein-DNA RFP
RestrictionMapper
Riboswitching
RNA RNAi - Dicer
Rolling-circle Am Run-On Transcription
Sequencing: dideoxy Sequencing: maxim & Gilbert
Sequencing: Multiplex Polony
Separation Si/tRNAs
SNP SOE PCR
Sorting Tetramer Assay
Spectroscopy Transfection
Two-Hybrid
Reverse Two Hybride Three-Hybrid
Vaccines Vectors
NAR links WebQTL

Departments

Anatomy Big Picture Biol.
Cardiovascular Cheminformatics
Chemistry Computational Biol.
Development Dev.Biol|Cinema
Drug Discovery

Gene Annotation

Gene Ontology. Gene Therapy
Immunology Medicine
Microbiology Neurobiology
Organism Biol. Physics
 System Biol. Virology

Groups-BioPharm-Regulatory

Alliances Associations
ATP Bio-Computing
BioPharm Career
Consortiums Foundations
Funding Institutes
NCRR NIST
Organizations Patents
Policy/Legislation Database
Publishers 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 
ADP-ribosylation
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 Methylation. DNA Demethylation
DNA Repair
DNA Repl. Drug Resistance
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 Hypoxia-Cancer
Histones-DNA HS
Immune deficiency Immunity Link
Imprinting Interactomes
LCR Inflammation
Memory Memory long-term
Life-or-death
Memory Cells Methy. Imprint
Modular Feedback Nitrosylation
Noise in gene expression
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
Protein Folding Protein Unfolding
Prot. Methyl. Protein-Prot.
Regeneration
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 -VAMP8
Reproduction Respiratory

Cell

B Cell

b Cell Formation

Cell Lines CTL
Cultured Cells Dendritic
NK Stem Cells
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
P-bodies Peroxisome

Vehicle

Argosomes POD

 Factory

Endoplasmic Reticulum Gene Expression

Machines

Chromatin Assembly & Remodeling CeramideTrafficking
  Protea -somes

Motor

Dyneins Kinesin (Movies)
Myosin Prestin

Molecule - Complex - Function

7SK Agrin
Alpha-Synuclein 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
Parkin/DJ-1
Peptide Nucleic Acid Pink1/UCHL1
Poly(A) polymerase Preinitiation C
Prot. Degrad Protein-Prot
Protein-DNA Protea -somes
RAR  Pyr Dehydog
Reelin P-TEFb
Ribosome Ribozyme
Riboswitch RIP140
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 Transcriptional Rheostat
Transcriptome
Transporters Ubiquitin-Endo
Ubi-Pr-VCP
Ubiquitin Ligase Ubiquitin-Trans
VAMP8

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

Alzheimer's 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

CHEMINFORMATICS
Databases Cheminformatics

Projects Cheminformatics

Resources

CHEMICAL GENETICS
 
 
SYSTEM BIOLOGY
Publication

GENOME BROWSERS

GENOME BROWSERS
 

GENE TRAP

GENE TRAP



 

 
Cis ELEMENTS
DATABASES-ciselemments

SERVICES -ciselemments

PROJECTS-ciselemments

||||Cis elements@Wheaton College

PORTALS (more links)-ciselemments

PUBLICATIONS

RNA & RNAi Worlds
For larger collection of Links see 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

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

  • Proteomic Reviews (Nature)
  • 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

 
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.

Homophila - utilizes the sequence information of human disease genes from the NCBI OMIM (Online Mendelian Inheritance in Man) database in order to determine if sequence homologs of these genes exist in the current Drosophila sequence database (FlyBase).

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; Dell

Policy/Legislation Database Patents: Delphion; DNA; EPO; Micro; U.S.

BioPortfolio; Hoover's

Movies MagPortal Sounds

Address of academic or Biopharma colleague:

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

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

Funded Researcher Databases

Management - Grants

 

News Granting

RFAs, PGAs etc.

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
Animated 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

A| B| C| D| E| F| G| H| I| K| L| M 

 N| O| P| R| S| T| V| W| Y| Z|

Align nucleic acids or protein sequence via:

AmphibiaWeb
Anticancer agents
ATCC
Alt-Splicing Catalog
Apoptosis B
BioMagResBank
A Repository for Data from NMR Spectroscopy on
Proteins, Peptides, and Nucleic Acids (Department of Biochemistry University of Wisconsin-Madison).
Biozon.org - Unified view of data from SwissProt, PDB, BIND, Genbank, KEGG and other databases.
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.
Bovine
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) C
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
Cytokines
Cytomer D
D. discoideum
Disease
  • Encyclopedia
  • 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).
  • Homophila - utilizes the sequence information of human disease genes from the NCBI OMIM (Online Mendelian Inheritance in Man) database in order to determine if sequence homologs of these genes exist in the current Drosophila sequence database (FlyBase).
DNA sequences alignments can be done rapidly with
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

Drug Resistance
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 F
FingerPRINTScan

FishBase

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

Gene-finding & organizing software Site

Read about it

  • 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

Data Mining

Gene Annotation sites & Tools

Gene Data Mining


More 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

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)  H
 
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

Homophila - utilizes the sequence information of human disease genes from the NCBI OMIM (Online Mendelian Inheritance in Man) database in order to determine if sequence homologs of these genes exist in the current Drosophila sequence database (FlyBase).
HotMolecbase targets for drugs    

Human - Mouse           

Hybridoma Bank   I
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.).           L
LocusLink? - curated sequences, description & alphabetic lists of genetic loci, search function,  related links, etc. (NCBI, USA). M
M
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 & Mutagenesis
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).

N

N
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
O
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.   

 

P
p53 mutation database
Pancreas
  • Endocrine Pancreas Consortium (EPConDB)
Pathways
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
Phenomic database
PhysioNet - physiologic signals and related open-source software
Policy/Legislation Database
Primase

PRINTS

PROMISE - The Prosthetic groups and Metal Ions in Protein Active Sites Database Version 2.0 (U. of Leeds).
PDBsum: A database of the known 3D structures of proteins and nucleic acids
Protein MSPcrunch: A BLAST post-processing filter - searches SWIR (non-redundant data bases of SwisProt, SP-TREMBL, & WormPep)(Sonnhammer &, Durbin).
Prostate Expression Database

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 Database Search Engine - Protein DBS system provides Protein Global-to-Global Tertiary Structure Matching.

Protein Kinases

Proteome Analysis
Protein sequence alignments can be done rapidly with
PSORT - Protein Cellular localization sites in Cells
Puffer Fish

 

R
Rat Databases
Rat Genomic Tools
Reactome: biological processes knowledgebase
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 - see RNAi@ elegansNet for additional links
S
Sanger Center Sitemap
SCOP Structural Classification of Proteins
Human Serum Proteome

SNPs

Sequencing Centers

Signal Transduction - CSNDB
Signal Transduction Pathways
S/MAR transaction

SRS6-EBI A unified db

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

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
V
VAST - Searches for similarity between proteins

Vectors

Virology
W
WormBase
Worm db links
X
Xenopus
Y
Yeast
Z
Zebrafish

Zinc - a free database of commercially-available compounds for virtual screening. ZINC contains over 3.3 million compounds in ready-to-dock, 3D formats.

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:

  Align via

 Analyze it at one site via:

  • SMS - Sequence Manipulation Suite 2

  • 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

DNA sequence alignment

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

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:

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 & sequence manipulation 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).

  • SMS - Sequence Manipulation Suite 2

  • 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

 

Ontologies

Ontologies - A series of Open Access refereed research articles describing new research with ontologies are freely available online. The articles describe mouse and mammalian phenotype ontologies, an ontology for cell types, an ontology for annotating different types of data pertinent to anatomy, a sequence ontology for annotating genomes, and a relation ontology that can promote interoperability of ontologies (2004 - 2005). Also see:

 

Gene Annotation-related

sites


Gene Annotation Format & Tools

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

Data, mining, processing, & probe design

Data Standard

Standards at last!