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/

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

MEME/MAST

http://meme.sdsc.edu/meme/intro.html

DNA Gibbs sampler

http://bayesweb.wadsworth.org/cgi-bin/gibbs.8.pl?data_type=DNA

AlignACE

http://atlas.med.harvard.edu/cgi-bin/alignace.pl

BioProspector

http://ai.stanford.edu/~xsliu/BioProspector/

FootPrinter (Phylogenetic footprinting)

http://genome.cs.mcgill.ca/cgi-bin/FootPrinter3.0/FootPrinterInput2.pl

PhyloGibbs (Phylogenetic footprinting)

http://www.phylogibbs.unibas.ch/cgi-bin/phylogibbs.pl

Alignment software

Global

ClustalX

http://www.clustal.org/

T-COFFEE

http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi

MUSCLE

http://www.drive5.com/muscle/

MAFFT

http://align.bmr.kyushu-u.ac.jp/mafft/online/server/

DIALIGN

http://bibiserv.techfak.uni-bielefeld.de/dialign/

Local

BLAST

http://blast.ncbi.nlm.nih.gov/Blast.cgi

FASTA

http://www.ebi.ac.uk/Tools/fasta33/index.html

LALIGN

http://www.ch.embnet.org/software/LALIGN_form.html

Alignment editors

JalView

http://www.jalview.org/

BioEdit

http://www.mbio.ncsu.edu/BioEdit/BioEdit.html