Selected Biological Resources on the Web

(Reviews by Tufts University Genomics and Bioinformatics Students)

Seq analysis Portals
Genome portals
cDNA expression
transcription databases
signalling pathways
motifs and domains
Reagents and protocols (PCR)
Disease related
Literature analysis

Links to Databases

2007 NAR Database issue

2006 NAR Database issue

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 (review)

Molecular 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

Portals for sequence analysis

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

Gene Portals (review )

GeneCards: human genes, proteins and diseases (Weizmann) The GeneCards database offers concise informationabout human genes (and their mouse homologs), with a focus on their cellular functions and medical as (added 2000/05/02)

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)

Genew: Searchgenes
official human gene names with aliases
Bioinformatics Harvester - consolidated gene portal site (review)

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. (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

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 ) (review2)

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)

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

Signaling databases (review)

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 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  (review)
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

PRIME -  Japanese Kinase pathway database that includes text and experimental data

iPath  interactive visual collection of 225 biological pathways from Invitrogen - free

reactome - manually curated database of pathways

Igenuity Pathway Analysis - commercial pathway analysis tools

jDesigner - opensource pathway design and simulation tool


Motif and protein family Databases

InterPro Home integrated Pfam, prints, and prosite database (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)

PhosphoSite – curated database of phosphorylation sites in human and mouse proteins.

Vast - search for proteins based on 3D structure similarity. (review)


Reagents, Protocols, and Supplies (review)

BioSupplyNet search for supplies and reagents

Biocompare - The Product Experts commercial consumer product guide for the Life Sciences with user reviews (review ) - - 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

The World Famous PCR Jump Station PCR links (review )

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

PrimerBank - This is Brian Seed's bank for validated PCR primers for all mouse and human genes (recommended)


RNAi  (review)

siDirect  - siRNA design site that has sophisticated rules with off target screening

SIDE – SIDE another more sophisticated siRNA design site -  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

DKFZ Boveri-Group Signaling -> eRNAi specs <-  another RNAi design site optimized for off target effects 

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
Rembrandt Database -  NCI brain tumor database


Literature Related

Prestige Factor alternate journal ranking service and database

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)

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
automated system for translating expression data into funtional profiles (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)

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.

David - NIH suite of gene annotation tools - includes a gene ID converter

Genesifter - commercial online microarray analysis with free trial  (review)



Chimera - free 3D molecular design software (review)

Database of Genetic Analysis software -  focuses on linkage analysis - The Biomedical Software and Database Search Engine
Searchable database of bioinformatics software  

Other Links