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/

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

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

https://epd.epfl.ch//index.php

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

Virtual Footprint

https://www.prodoric.de/vfp/

Online motif discovery tools

MEME/MAST

https://meme-suite.org/meme/tools/meme

AlignACE

https://arep.med.harvard.edu/mrnadata/mrnasoft.html

BioProspector

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

PhyloGibbs (Phylogenetic footprinting)

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

Alignment software

Global

ClustalX

http://www.clustal.org/

T-COFFEE

http://tcoffee.crg.cat/

MUSCLE

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

MAFFT

https://mafft.cbrc.jp/alignment/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

Other links

Radio

Catalunya Radio

http://www.catradio.cat/

Catalunya Radio (archives)