Nucleic Acids Research 2003 Webserver issue -Annual issue of NAR devoted to biological webservers
Nucleic Acids Research 2004 Database issue - Annual NAR database issue
Nucleic Acids Research Database list - compilation and categorization of databases published in NARMolecular Biology Databases Weizman links to databases (Review )
Blueprints portal Web search though bininformatics sites using hotbot
Bioinformatics portal recently enhanced bioinformatics portal (review )
Catalog of
Databases
French database of databases
CuraToolsTM - Home Page integrated web based sequence analysis (review )
SDSC Biology Workbench integrated analysis portal (review )
LabVelocity--locate scientific products, protocols, literature and news. portal for products, protocols, info, and has a literature search agent (review )
nodalpoint portal for discussions of biological issues (review )
SeWeR: Sequence Analysis using Web Resources javascripted pages for integration of web based sequence analysis ( review )
GeneQuiz - Home page site for automated sequence analysis and function discovery
ExPASy
- proteomics Tools Swissprot online proteomics tools - protein
fingerprinting (review)
ABIM Online analysis tools large list of links to online sequence analysis tools
Algorithms, thermodynamics and databases for RNA secondary structure. links to RNA structure software and info
IUBio Archive
for Biology data and software including Eugene (
review
)
2can - bionformatics
tutorials (review)
KEGG Encyclopedia kyoto KEGG integrated database (added 2000/05/03) (revew )
BODY MAP database of tissue specific gene expression (added 2000/05/03) ( review )
About GXD Homepage of the mouse gene expression database - literature and EST based mostly - could be better (review )
vector database database of vector sequences (This DB is not active and is looking for a new home)
Proteome Databases Home Page YPD (yeast) and WormPD databases some human ( review ) (recent changes)
Human Genome Working Draft UCSC human genome with browser
Ensembl
Genome Server integrated gene sequence viewer from EBI with
extensive
annotations (review)
Incyte gene databases search Incyte databases
SGD - yeast genome site (review)
Sacch 3D - Structural information for yeast proteins ( review )
Rat Genome - Homepage of the rat
genome
project (review
)
Flybase - the fly genome (review)
Human Genes - full length cDNAs source for purchase of >10,000 full length cDNAs
KDRI Databases databases of full length cDNAs from Japan
Mammalian
Gene Collection - NIH Homepage of mammalian gene collection.
Repository
of full length cDNAs. Unclear if the cDNAs are in expression vectors. (review)
Orbigen: Enabling the Proteomics Revolution database of protocols, links, and full length cDNAs for $499 ( review )
pORF vectors : The hottest genes ready for subcloning commercial cDNA expression vector library
Welcome to GeneCopoeia(TM) Another full length gene cloning company and database about $750/clone
Welcome to HUGE protein database cDNA sequencing project of full length human cDNAs
Transcription Regulatory Regions Database (TRRD) russian transcription factor DB site (review )
TRANSFAC - The Transcription Factor Database German site for TRANSFAC (now part of biobase) (review )
SAGE Home Page homepage for analysis of gene expression by SAGE
Cancer Genome anatomy project links to databases on cancer genes (review )
Sequence Alerting System Sequence Alerting System -The sequence alerting system in its present form will search each day in several databases for news on homologies.
BioMail Login automated medline searching bot
Bionews - Bioinformatics email forum with many new service announcements
TheScientificWorld
another abstract alerting service
MGI 2.3.2 - Mouse Genome
Informatics
(MGI) Main Menu Jackson labs mouse genome database (added
2000/05/02)
MPD - Welcome to the Mouse Phenome Database mouse genotype phenotype relations
SEBI mouse related homepage mouse links (added 2000/05/03)
TBASE transgenic and targetted mutation database (added 2000/05/02)
Lexicon Genetics Mining the Genome omnibank knockout database (review )
Nagy
Lab Databases of Cre transgenic line and floxed genes (
review )
trangenic
mouse links michigan collection of links on mice
SPAD : Signaling PAthway Database japanese signalling pathway database (review )
Protein Kinase Resource Compendium of information on the protein kinase family of enzymes ( review )
BioCarta - Charting Pathways of Life user contributed molecular pathways (review )
BIND - The Biomolecular Interaction Network Database Homepage of the BIND project for identifying protein interactions ( review )
Links to protein interaction databases - Links from the BIND site
Database of Interacting Proteins (DIP) User supported database of proteins known to interact ( review )
PubGene Database of gene interactions derived from automated literature searches (now pubgene.com available) (review ) (review2 )
Physiome Sciences, Inc. company that specializes in cell modeling including signal transduction models (review )
STRC Biocomputation Group Homepage of cell modeling group (review )
BBID pathways database NIH searchable database of pathways and such (review )
PRINTS protein fingerprint database (review )
The Brutlag Bioinformatics Group - Projects emotif etc (emotif review )
MEROPS good protease database (Review ) (changes)
PhosphoBase - A database of phosphorylation sites phosphorylation site database
Scansite Menu Lew Cantley's protein motif scanner (review )
Wnt gene homepage - everything Wnt (review ) (review2 )
G protein receptor Database - (review )
Glycoforum Everything about glycoproteins (review )
NLSdb - database of nuclear localization sites
Human Protein Reference Database
- manually curated database of protein domains and interactions from
Hopkins (review)
iHOP - text
mining based protein database of A. Valencia
STRING – database of known and predicted protein-protein interactions in 179 species.
ESPSearch
–
searches DNA, RNA, or protein sequences for specific target sequences. (review)
RESID Database – database of protein modifications, with graphics and interfaced with EMBL-EBI.
Phosphorylation
Site – database of prokaryotic proteins phosphorylation.
PhosphoELM -
another database of phosphorylation sites (review)
Biocompare - The Product Experts commercial consumer product guide for the Life Sciences with user reviews (review )
Biowire.com - - Definitive resource of knowledge and tools biological researcher site for user reviews of lab equipment and software ( review )
GUTHRIE cDNA Resource, Guthrie Research Institute, Human CDNA, CDNA full length cDNA repository of signalling genes with an emphasis on G-proteins
metazoa > Research Management Systems web based lab notebook and protocol library (probably defunct) (review )
Molecular Biology Techniques Forum active searchable molecular methods forum (review )
Abcam- database of commercial antibodies ( review )Openwetware -
MIT wiki based protocols site
Protocols Online -
online protocols with discussion boards
DrugBank
Homepage database of drugs
PCR related
BioMath
- Tm Calculations for Oligos PCR and oligo Tm calculator
Virtual
PCR
site for testing PCR primers against genome for non specific
amplification (review)
Primer3
Input (primer3_www.cgi v 0.2) pcr primer picking site at
whitehead
Gene
Quantification & real-time PCR or kinetic RT-PCR site devoted
to
real time PCR for quantitating mRNA ( review
)
Real
time PCR tutorial - from South Carolina
genscript siRNA design center - site for siRNA design with unique sequence searching
Drosophila RNAi screening center
-
Perrimon fly RNAi screening service and data
DKFZ
Boveri-Group Signaling -> eRNAi specs <- another
RNAi design site optimized for off target effects
Tumor Gene
database
- organized literature information about known tumor genes (
review ) (revew
2)
Faculty of 1000
Distributed
article relevance ranking service (review)
Acromed Definitions of biomedical acronyms
Medline Workbench - Usa Mirror CSH portal to the journals
Medstract server - beta version of server for biorelations
quosa - software for full text
retrieval
and literature searching (review)
iPapers
- Mac based pubmed and pdf software
Papers - Mac base
pubmed and literature organizer
Database of teaching resourses for Biology - BEN
MedMiner
a sophisticated but complex query system for pubmed and genecards (
review )
GoPubMed
- Ontology based literature search (Biotec/TU-Dresden)
pubmed searching using Go ontology
Google
Scholar - full text searching of scholarly articles (review)
Chilibot – PubMed
literature-based search for relationships between genes, proteins, and
keywords of researcher’s interests.
eTBLAST
- Pubmed search based on text similarity rather than keywords.
cBioc - hybrid text mining
collaborative annotation project
Microarrays (review)
Pandora - analysis of protein sets based on keywords from annotations
Cancer gene expression - John Weinstein lab site with microarray data and more
GenePublisher - website for automated microarray analysis
PAM - excel add-in for predication analysis of microarrays
GOSurfer
- software that classifies gene clusters based on GO annotations
(Windows)
Chimera
- free 3D molecular design software (review)
Database
of
Genetic Analysis software - focuses on linkage analysis
BioWareDB.org
- The Biomedical Software and Database Search Engine
Searchable database of bioinformatics software