Gibbs Motif Sampler 3.10 – Identify Motifs, Conserved Regions, in DNA or Protein Sequences

Gibbs Motif Sampler 3.10

:: DESCRIPTION

The Gibbs Motif Sampler will allow you to identify motifs, conserved regions, in DNA or protein sequences.

::DEVELOPER

Wadsworth Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows with Cygwin/MacOsX

:: DOWNLOAD

 Gibbs Motif Sampler

:: MORE INFORMATION

Citation

Neuwald AF, Liu JS, and Lawrence CE. (1995)
Gibbs motif sampling: detection of bacterial outer membrane protein repeats.
Protein Sci 4(8):1618-1632. PubMed: 8520488.

PCPMer 3.5.6 – Determine Conserved Regions in multiple Sequence Alignments

PCPMer 3.5.6

:: DESCRIPTION

PCPMer (Physical Chemical Property Based Motif Analyzer ) is a software package for determining conserved regions in multiple sequence alignments. The software represents each of the 20 naturally occuring amino acids by five quantitative descriptors and can detect motifs (short regions of significant conservation) in aligned sequences based on relative entropy or physicochemical similarity. It can be then used to search for related proteins in a protein sequence database and map the variability data on a 3D structure (to make a stereophysicochemical variability plot, or SVP). Such plots are particularly useful for identifying the spatial relationships of highly conserved or variable residues to one another.

::DEVELOPER

 PCPMer Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PCPMer

:: MORE INFORMATION

Citation:

Schein, C.H., Zhou, B. and Braun, W.
Stereophysicochemical variability plots highlight conserved antigenic areas in Flaviviruses.
Virol. J. Apr 21;2(1):40, 2005

 

M-GCAT 2.0 beta – Detect Highly Conserved Regions in Multiple Genomes with Rearrangements and Repeats

M-GCAT 2.0 beta

:: DESCRIPTION

M-GCAT is a tool for rapidly visualizing and aligning the most highly conserved regions in multiple (typically prokaryote) genomes. M-GCAT is based upon a highly efficient approach to anchor-based multiple genome comparison using a compressed suffix graph and thus can construct multiple genome alignment frameworks in closely related species usually in a few minutes. A couple of important limitations include (1) input sequences MUST be assembled, and (2) the comparison is reference-sequence biased.

::DEVELOPER

 the Algorithmics and Genetics Group 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 M-GCAT

:: MORE INFORMATION

Citation

T. Treangen and X. Messeguer.
M-GCAT: Interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species.
BMC Bioinformatics 2006, 7:433.