Campus is closed on Wednesday, February 20th due to inclement weather.
Skip to Main Content

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