:: DESCRIPTION
MixMir is a program for finding microRNA motifs using gene expression and 3′ UTR sequence data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nucleic Acids Res. 2014;42(17):e135. doi: 10.1093/nar/gku672. Epub 2014 Jul 31.
MixMir: microRNA motif discovery from gene expression data using mixed linear models.
Diao L, Marcais A, Norton S, Chen KC
:: DESCRIPTION
MotifIndexer is a comprehensive strategy for de novo identification of DNA regulatory motifs at a genome level.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ma S, Bachan S, Porto M, Bohnert HJ, Snyder M and Dinesh-Kumar SP. (2012)
Discovery of stress responsive DNA regulatory motifs in Arabidopsis.
PLoS ONE 7:e43198
:: DESCRIPTION
CompareProspector is a sequence motif-finding algorithm which extends Gibbs sampling by biasing the search in promoter regions conserved across species. Using human–mouse comparison, CompareProspector correctly identified the known motifs for transcription factors Mef2, Myf, Srf, and Sp1 from a set of human muscle-specific genes. It also discovered the NFAT motif from genes upregulated by CD28 stimulation in T cells, which suggests the direct involvement of NFAT in mediating CD28 stimulatory signal. Using C. elegans–C. briggsae comparison, CompareProspector found the PHA-4 motif from pharyngeally expressed genes and the UNC-86 motif from genes known to be regulated by UNC-86. CompareProspector outperformed many other computational motif-finding programs tested, demonstrating the power of comparative genomics-based biased sampling in eukaryotic regulatory element identification.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S.
Eukaryotic regulatory element conservation analysis and identification using comparative genomics.
Genome Res. 2004 Mar;14(3):451-8.
:: DESCRIPTION
MotifCut is a DNA motif-finding algorithm using a Maximum Density Subgraph.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2006 Jul 15;22(14):e150-7.
MotifCut: regulatory motifs finding with maximum density subgraphs.
Fratkin E, Naughton BT, Brutlag DL, Batzoglou S.
:: DESCRIPTION
ALSE (ALl SEquences) compares favorably against common motif-finding programs such as SeedSearch and MEME in all cases and performs very well, especially when each input sequence contains more than one binding site.
::DEVELOPER
Bioinformatics Research Group of Hong Kong University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2006 Sep 15;22(18):2217-23. Epub 2006 Jul 26.
Finding motifs from all sequences with and without binding sites.
Leung HC, Chin FY.
:: DESCRIPTION
AlignACE (Aligns Nucleic Acid Conserved Elements) is a program which finds sequence elements conserved in a set of DNA sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hughes, JD, Estep, PW, Tavazoie S, & GM Church,
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae,
Journal of Molecular Biology 2000 Mar 10;296(5):1205-14.
