Selected Biological Resources on the Web
(Reviews by Tufts University Genomics and Bioinformatics Students)
Seq analysis
Portals
Genome
portals
cDNA
expression
transcription
databases
Bots
mouse
signalling
pathways
motifs and
domains
Reagents and
protocols
RNAi
Disease related
Literature
analysis
microarrays
software
Links to Databases
2005 NAR Database issue
Nucleic Acids Research, Volume 26, Issue 01 Issue of NAR devoted to molecular biology databases
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 NAR
Expasy links page Extensive organized list of Bio links with an emphasis on genomic database
British Bioinformatics Resource links to web resources
Molecular Biology Databases Weizman links to databases (Review )
BioBencHelper list of links to useful bench stuff like g force vs rpm and techniques ( review )
Blueprints portal Web search though bininformatics sites using hotbot
Bioinformatics portal recently enhanced bioinformatics portal (review )
Catalog of Databases French database of databases
Portals for sequence analysis
Labonweb - commercial sequence and 2D gel analysis portal (review )
CuraToolsTM - Home Page - integrated web based sequence analysis (review )
https://www.doubletwist.com/ - remove; website defunct
SDSC Biology Workbench integrated analysis portal (review )
LabVelocity - commercial software for sequence analysis (Jellyfish); also portal for products, protocols,
information, bioinformatics links; has 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; now includes Savvy, an integrated, web-based plasmid drawing software ( review )
GeneQuiz - Home page – site for automated sequence analysis and function discovery; requires installation
of other software.
ExPASy - proteomics Tools – SwissProt online proteomics tools - protein fingerprinting
Bio-Web: Molecular Biology, Cell Biology, Mac Software and more... Molecular biology portal with many
links and software downloads - Mac orientation Could not update or check; no access to Mac
ABIM Online analysis tools – genomic and proteomic sequence analysis tools
Algorithms, thermodynamics and databases for RNA secondary structure - links to RNA structure software
and info; last up-dated 10.17.03
IUBio Archive – for biology data and software including euGenes ( review )
Gene Portals (review )
GeneCards: human genes, proteins and diseases (Weizmann) The GeneCards database offers concise
information about human genes (and their mouse homologs), with a focus on their cellular functions and
medical applications. Database includes:
GeneNote – microarray-determined database of human genes and expression profiles in healthy
tissues.
GeneAnnot – annotation of Affymetrix probe-sets for human genes.
GeneLoc – integrated map for each human chromosome (updated 1.13.05)
GeneTide – human mRNA and ESTs transcripts
KEGG Encyclopedia - integrated database of biological pathways, reactions, therapeutic relations (review )
BODY MAP - database of human and mouse tissue specific gene ( review )
GXD – mouse gene expression database - literature and EST based mostly - could be better (review )
vector database - database of vector sequences (5-2005 transferred to Saccharomyces Genome Database)
BioBase Biological Databases -- formerly Proteome and Incyte gene databases ( review ), commercial
databases of mammalian protein-protein interactions, human gene sequence and expression, transcription
factors, and signal transduction.
Human Genome Working Draft - UCSC human genome with browser
Ensembl Genome Server - integrated gene sequence viewer from EBI with extensive annotations
Incyte gene databases -- now owned by BioBase Biological Databases.
HCNetDat – Affymetrix DNA microarray database, containing annotation for genes from Incyte’s mouse
and human libraries, etc, microarray comparisons, and human-mouse ortholog search.
SGD - yeast genome site
Sacch 3D - Structural information for yeast proteins ( review )
Rat Genome - Homepage of the rat genome project (review )
Genew: Searchgenes – official human gene names with aliases
Chilibot – PubMed literature-based search for relationships between genes, proteins, and keywords of
researcher’s interests.
Osprey – network visualization program of Gene Ontology annotated interaction data.
BioRag – database to analyze gene expression patterns for human and mouse genomes in terms of gene and
protein function and pathways, protein interactions, and disease.
Full length cDNA expression vectors (review )
Harvard Institute of Proteomic Home of Ed Harlow's full length cDNA expression cloning project
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.
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
KDRI Databases
databases of full length cDNAs from Japan
Open Biosystems: Expanding Access > Home
source for image clones and full length cDNAs and shRNA libraries
Transcription Databases
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL paper on transcription factor
databases (added 2000/05/02)
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 )
Genomatix Software GmbH
site for finding transcription factor binding sites - easy to use (mostly pay acess now)
TFSearch - search for Transcription factor binding sites in a sequence
Bots (review )
PubCrawler Home Page automated medline searches
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
Mouse Related (review )
JAX Mice- Mouse Models for Research This site describes the world's most comprehensive offering of
genetically defined mice for biomedical research. (added 2000/05/02)
MGI 2.3.2 - Mouse Genome Informatics (MGI) Main Menu Jackson labs mouse genome database (added
2000/05/02)
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 )
Signaling databases
Transpath Home Page pathways database (now at Biobase) (review )
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 )
AfCS-Nature Signaling Gateway - home
alliance for cell signalling site
BRITE Home Page
another protein protein interaction database from Japan
Gene Regulation
From the developers of transpath, several signalling related databases with both free and pay
versions
Genepath - Outstanding XML based tool for modeling and analyzing pathways
PRIME - Japanese Kinase pathway database that includes text and experimental data
Motif and protein family Databases
InterPro Home integrated Pfam, prints, and prosite database (review )
PRINTS – protein fingerprint database (review ); now linked with InterPro
The Brutlag Bioinformatics Group - proteome databases and search engines for ORF conserved regions,
motifs, and sequences; 3D structure visualization. (emotif review )
MEROPS – good protease database (Review )
PhosphoBase - database of eucharyotic phosphorylation sites, now hosted by EMBL
Scansite Menu – Lew Cantley's protein motif scanner (review ) new version 12.17.04.
Wnt gene homepage - everything Wnt (review ) (review2 )
G protein receptor Database - GPCR databases, including Frank Kolakowski’s GCRDb which is no longer
accessible (review )
Glycoforum – Everything about glycoproteins (review )
NLSdb - database of nuclear localization sites (accessible but seems out-of-date)
Human Protein Reference Database - manually curated database of protein domains and interactions from
Hopkins
STRING – database of known and predicted protein-protein interactions in 179 species.
ESPSearch – searches DNA, RNA, or protein sequences for specific target sequences.
RESID Database – database of protein modifications, with graphics and interfaced with EMBL-EBI.
Phosphorylation Site – database of prokaryotic proteins phosphorylation.
PhosphoSite – curated database of phosphorylation sites in human and mouse proteins.
Reagents, Protocols, and Supplies
BioSupplyNet search for supplies and reagents
Biocompare - The Product Experts commercial consumer product guide for the Life Sciences with user
reviews (review )
LabVelocity (formerly Biowire)– Definitive resource portal for biological information, protocols, products,
literature software ( review )
UMR cDNA Resource Center - commercial repository of full length cDNA of signaling genes with an
emphasis on G-proteins (in agreement with Guthrie Research Institute).
metazoa > Research Management Systems – apparently defunct; no website found by Google-search
(review )
Molecular Biology Techniques Forum - active searchable molecular methods forum, with protocols
(review)
The World Famous PCR Jump Station PCR links (review )
Gene Quantification – quantitative gene expression analysis using real-time qPCR and qRT-PCR. ( review
)
Abcam- database of commercial antibodies ( review )
protocol on-line- sites for submitting protocols online; appears to replace former MIT website iProtocol.
bioProtocol – protocol website with archive section for protocols of interest; also retail site for software,
books, and lab equipment.
Bio-Web – cell and molecular biology tools and resources as well as portal for commercially available
bioinformatics tools, software, and instruments.
RNAi
siDirect - siRNA design site that has sophisticated rules with off target screening
SIDE – SIDE another more sophisticated siRNA design site
http://www.dharmacon.com/ - major siRNA supplier with siRNA tools
SVM for RNAi design
web based RNAi design program using support vector machine
genscript siRNA design center - site for siRNA design with unique sequence searching
Whitehead RNAi design center
Drosophila RNAi screening center - Perrimon fly RNAi screening service and data
Disease Related
GeneDis page Human genetic disease database - limited diseases represented ( review )
Tumor Gene database - organized literature information about known tumor genes ( review ) (revew 2)
Cancer Genome anatomy project homepage
NIH cancer genome expression and aberation and reagent database
Literature Related
Prestige Factor alternate journal ranking service and database
Faculty of 1000 Distributed article relevance ranking service
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
Database of teaching resourses for Biology - BEN
MedMiner a sophisticated but complex query system for pubmed and genecards ( review )
Microarrays
Gene expression databases and analysis tools – NCGR table of gene array databases and analysis tools
(annotated - good)
SMD Microarray Resources : Software & Tools – Stanford links to microarray analysis software
SOURCE Batch Search – Stanford source metaserach, extracts selected information from databases about
groups of genes
Web resources on Gene Expression and DNA Microarray Technologies – EBI microarray links page
OntoExpress – automated system for translating expression data into funtional profiles
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)
Software
Chimera - free 3D molecular design software
Database of Genetic Analysis software - focuses on linkage analysis
POLYVIEW – commercially-available visualization software program
NRCAM -- software for cell analysis and compartmental modeling to specify topology and geometry of
biological compartments, molecular characteristics, and relevant interaction parameters of biological
compartments.
Other Links