Sequence, Protein, and Annotation Websites

Functional Annotation and Analysis Tools
Sequence Databases
Protien Databases and Information
Text Mining
General References

Functional Annotation and Analysis Tools

BioCarta
Interactive informational website for Life Scientists.
Search for gene information by gene name, browse pathways, and download pathway tools to create your own maps
http://www.biocarta.com/index.asp

The Dragon Database
Pevsner Laboratory
Kennedy Krieger
Access to a number of bioinformatic tools, including a flexible annotate tool. The annotate tool allows you to append multiple types of biological information to large lists of genes, defined by Genbank accession numbers. The DragonView suite of tools can then be used to visualize your gene expression data in light of the information that you derive from the annotate tool.
http://pevsnerlab.kennedykrieger.org/dragon.htm

Genecards
Weizmann Institute of Science
GeneCards is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others.
This is an Interactive site designed to provide information on human genes (search by name or symbol), protiens, and diseases.
http://bioinfo.weizmann.ac.il/genecards/
http://genome-www.stanford.edu/genecards/
http://nciarray.nci.nih.gov/cards/index.html

Gene Ontology Consortium
The goal of the Gene Ontology^TM Consortium is to produce a dynamic controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. The three organizing principles of GO are molecular function, biological process and cellular component.
http://www.geneontology.org/

GenMAPP - Gene MicroArray Pathway Profiler
Gladstone Institutes, UCSF
A computer application designed to visualize gene expression data on maps representing biological pathways and groupings of genes.
You can use GenBank IDs or SwissProtIDs
http://www.genmapp.org/

Kyoto Encyclopedia of Genes and Genomes
The Bioinformatics Center, Institute for Chemical Research, Kyoto University
The Kyoto Encyclopedia of Genes and Genomes (KEGG) is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene catalogs produced by genome sequencing projects
You can search using EC numbers, compound numbers, gene names, or accessions.
http://www.genome.ad.jp/kegg/

NETAFFX Analysis Center
Affymetrix
Santa Clara, CA
The NetAffx Analysis Center enables researchers to correlate their GeneChip® array results with array design and annotation information.
You can use Affymetrix Array Names, probe set ids, public database numbers (UniGene,RefSeq,GenBank), or gene names
http://www.affymetrix.com/analysis/index.affx

Onto-Express
Wayne State University
Provides annotations from a range of databases.
You can use accession or cluster identification numbers, but not both.
http://www.openchannelfoundation.org/projects/Onto-Express
http://vortex.cs.wayne.edu/Projects.html

Stanford SOURCE database
The Stanford Online Universal Resource for Clones and ESTs (SOURCE) compiles information from several publicly accessible databases, including UniGene, dbEST, Swiss-Prot, GeneMap99>, RHdb, GeneCards, and LocusLink
http://source.stanford.edu/cgi-bin/sourceSearch

TIGR Software
The Institute for Genomic Research
An extensive suite of tools for gene finding/annotation, alignment, sequencing/finishing, microarray data management and analysis, and more.
http://www.tigr.org/software/

NIAID Applications
DAVID: Database for Annotation, Visualization and Integrated Discovery
http://david.niaid.nih.gov/
EASE: Expression Analysis Systematic Explorer
http://david.niaid.nih.gov/david/ease.htm

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Sequence Databases
dbEST
Expressed Sequence Tags Database
dbEST (Nature Genetics 4:332-3;1993) is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or Expressed Sequence Tags, from a number of organisms.
http://www.ncbi.nlm.nih.gov/dbEST/index.html

EMBL
The EMBL Nucleotide Sequence Database constitutes Europe's primary nucleotide sequence resource.
http://www.ebi.ac.uk/embl/

GenBank
http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html

LocusLink
LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci.
http://www.ncbi.nlm.nih.gov/LocusLink/

National Center for Biotechnology Information
http://www.ncbi.nlm.nih.gov

Reference Sequences
The NCBI Reference Sequence project
http://www.ncbi.nlm.nih.gov/locuslink/refseq.html

UniGene
UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters
http://www.ncbi.nlm.nih.gov/UniGene/

CGAP (Cancer Genome Anatomy Project)
The Cancer Genome Anatomy Project is an interdisciplinary program established and administered by the National Cancer Institute (NCI) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
The CGAP web site provides researchers with access to all CGAP data and biological resources. You can find genomic data for human and mouse, including expressed sequence tags (ESTs), gene expression patterns, single nucleotide polymorphisms (SNPs), cluster assemblies, and cytogenetic information.
http://cgap.nci.nih.gov/

Mouse Genome Informatics
The Jackson Laboratories
Search for records in MGD or GXD using accession IDs from these databases, or from any database that is cross-referenced in MGD or GXD (e.g., GenBank).
http://www.informatics.jax.org/
http://www.informatics.jax.org/mgihome/

Plant Genome Bioinformatics Group
Munich Information Center for Protein Sequences
http://mips.gsf.de/proj/thal/

Saccharomyces Genome Database
Stanford University
SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.
The website provides comprehensive gene/sequence search capabilities and extensive annotations output.
http://genome-www.stanford.edu/Saccharomyces/

Online Mendelian Inheritance in Man
John Hopkins University
This database is a catalog of human genes and genetic disorders.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

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Protein Databases and Information

HUGO Gene Nomenclature Committee
This group is dedicated to establishling unique and meaningful names to every human gene.
http://www.gene.ucl.ac.uk/nomenclature/

Protien Information Resource
Georgetown University
Sequence searching and protien identification.
http://pir.georgetown.edu

Swiss-Prot
The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.
Interactive search by AC, ID, description, gene name
http://us.expasy.org/

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Text Mining
MedMiner
The MedMiner filters will extract and organize relevant sentences in the literature based on a gene, gene-gene or gene-drug query.
http://discover.nci.nih.gov/arraytools/

PubMed
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed

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General References

Gene Array List Serve
http://www.gene-chips.com/gene-arrays.html

The Bioconductor Project
http://www.bioconductor.org/

Book reference with links to interesting websites
THE ANALYSIS OF GENE EXPRESSION DATA: METHODS AND SOFTWARE
edited by Parmigiani, G, Garrett, ES, Irizarry, RA and Zeger, SL.
Springer, NY
http://astor.som.jhmi.edu/hex/pgiz.html

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