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Useful Links

Below are some useful links in bioinformatics and genomics.

Genomic databases

Integrated Microbial Database @ DOE Joint Genome Institute

http://img.jgi.doe.gov/cgi-bin/pub/main.cgi

GenBank @ National Center for Biotechnology Information

http://www.ncbi.nlm.nih.gov/

Comprehensive Microbial Resource @ J. Craig Venter Institute

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

Regulatory databases

RegTransBase

Database of regulatory interactions on literature and expertly curated database of transcription factor binding sites

http://regtransbase.lbl.gov/cgi-bin/regtransbase?page=main

RegulonDB

Curated database of E. coli transcriptional regulation

http://regulondb.ccg.unam.mx/

PRODORIC

Prokaryotic database of gene regulation and systems biology

http://prodoric.tu-bs.de/

TRANSFAC

Knowledge base on transcription factors, their experimentally-proven binding sites and regulated genes

http://www.biobase-international.com/pages/index.php?id=transfac

DBD

Transcription factor prediction database

http://dbd.mrc-lmb.cam.ac.uk/DBD/index.cgi?Home

TRED

Transcriptional Regulatory Element Database (Human, Mouse, Rat)

http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=home

DBSD

The Drosophila Binding Site Database

http://rulai.cshl.org/dbsd/index.html

Promoter databases

CEPDB

C. elegans Promoter Database

http://rulai.cshl.edu/cgi-bin/CEPDB/home.cgi

SCPD

The Promoter Database of Saccharomyces cerevisiae

http://rulai.cshl.edu/SCPD/

CSHLmpd

Mammalian Promoter Database

http://rulai.cshl.edu/cshlmpd/

http://rulai.cshl.edu/cshlmpd/

EPD

The Eukaryotic Promoter Database

http://cmgm.stanford.edu/help/manual/databases/epd.html

PromEC

An updated database of E. coli mRNA promoters with experimentally identified transcriptional start sites

http://margalit.huji.ac.il/promec/

 

Online binding site search tools

PredictRegulon

http://210.212.212.6/prindex.html

Virtual Footprint

http://prodoric.tu-bs.de/vfp/

Online motif discovery tools

Global
Radio