Tag: CRM

PhylCRM 1.1 – Cis-regulatory Module (CRM) Prediction

PhylCRM 1.1

:: DESCRIPTION

PhylCRM is a new cis-regulatory module (CRM) prediction algorithm. PhylCRM combines data for individual motif occurances scored on an alignment using previously described MONKEY scoring sheme (Moses et al., Genome Biology 5, R98, 2004) into a single CRM prediction. PhylCRM can scan very long genomic sequences for candidate CRMs by quantifying both motif clustering and conservation across arbitrarily many genomes using an evolutionary model consistent with the phylogeny of the genomes.

::DEVELOPER

The Bulyk Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  PhylCRM

:: MORE INFORMATION

Citation

Nat Methods. 2008 Apr;5(4):347-53. doi: 10.1038/nmeth.1188. Epub 2008 Mar 2.
Systematic identification of mammalian regulatory motifs’ target genes and functions.
Warner JB, Philippakis AA, Jaeger SA, He FS, Lin J, Bulyk ML.

SCRMshaw – Genome-wide Supervised CRM Prediction

SCRMshaw

:: DESCRIPTION

SCRMshaw is a genome-wide CRM prediction program that learns parameters from a list of CRMs that regulates the same spatial/temporal gene expression pattern, and predicts CRMs with similar functionality genome-wide. The SCRMshaw program is designed for predicting CRMs in the genome sequence of model/non-model species given the known CRMs provided by users. Users can also choose three different scoring schemes to predict CRMs: IMM, PAC and HexMCD.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SCRMshaw

:: MORE INFORMATION

Citation:

Dev Biol. 2016 Aug 15;416(2):402-13. doi: 10.1016/j.ydbio.2016.06.031.
Redeployment of a conserved gene regulatory network during Aedes aegypti development.
Suryamohan K, Hanson C, Andrews E, Sinha S, Scheel MD, Halfon MS.

CRM 20111028 – Identification of Conserved Motif Modules

CRM 20111028

:: DESCRIPTION

The function of CRM is to get cis-regulatory modules about 522 transfac motifs at given specific cutoffs.

::DEVELOPER

Xiaoman Shawn Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Python

:: DOWNLOAD

 CRM

:: MORE INFORMATION

Citation:

Cai X, Hou L, Su N, Hu H, Deng M, Li X.
Systematic identification of conserved motif modules in the human genome.
BMC Genomics. 2010; 11:567.