Bioinformatics Links Directory : Gene Regulation

This section contains links to tools and resources for predicting gene regulation, such as promoter analysis.

MicroFootPrinter - (Found July 2, 2008 )

MicroFootPrinter identifies the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.
http://bio.cs.washington.edu/MicroFootPrinter.html

MicroInspector - (Found July 2, 2008 )

MicroInspector is a tool that detects miRNA (microRNA) binding sites in your input sequence by searching against databases of known miRNA binding sites.
http://mirna.imbb.forth.gr/microinspector/

miRU - (Found July 2, 2008 )

miRU is a tool that takes as an input a small miRNA sequence and then searches for complementary matches in TIGR plant-specific gene data sets to predict potential target genes.
http://bioinfo3.noble.org/miRU.htm

MoD Tools - (Found July 2, 2008 )

Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes; WeederH, a tool for detecting TFBS and regulatory regions from homologous genes; and RNA profile, a tool for secondary structure motif discovery in RNA sequences.
http://159.149.109.16/modtools/

MSCAN - (Found July 2, 2008 )

MSCAN takes as input one or more DNA sequences and a set of transcription factor binding site profiles. It then detects clusters of the binding sites in the sequences.
http://mscan.cgb.ki.se/cgi-bin/MSCAN

Match - (Found July 2, 2008 )

Match is a weight matrix-based tool which searches for putative transcription factor binding sites (TFBS) in DNA sequences. Registration at the site is free and is required to use Match.
http://www.gene-regulation.com/cgi-bin/pub/programs/match/bin/match.cgi

MADAP - (Found July 2, 2008 )

MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5' and 3'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).
http://www.isrec.isb-sib.ch/madap/

FootPrinter - (Found July 2, 2008 )

FootPrinter is a program for phylogenetic footprinting that identifies regions of DNA that are well conserved across a set of orthologous sequences in order to infer phylogenetic relationships.
http://bio.cs.washington.edu/software.html

FootPrinter3 - (Found July 2, 2008 )

FootPrinter3 is a web server for predicting transcription factor binding sites (TFBS) by using phylogenetic footprinting. FootPrinter3 extends the motif discovery algorithms of FootPrinter by making use of local multiple sequence alignment blocks when those are available and reliable, but also allowing finding motifs in unalignable regions.
http://genome.cs.mcgill.ca/cgi-bin/FootPrinter3.0/FootPrinterInput2.pl

g:Profiler - (Found July 2, 2008 )

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein namesIDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles.
http://biit.cs.ut.ee/gprofiler/