Tag: GMV

GMV 0.1 – Genome Majority Vote Gene Start Correction Software

GMV 0.1

:: DESCRIPTION

The GMV pipeline works as follows. Input is a set of genomes. The pipeline runs PRODIGAL gene predictions on all genomes, runs pan-reciprocal BLAST, and identifies ortholog sets. For a given set of orthologous genes, if the positions of the PRODIGAL selected starts coincide in a multiple sequence alignment, they are accepted. If they do not coincide, a consistent start position is sought where a majority of the highest-scoring PRODIGAL selected sites coincide. If such a position is found, it is accepted, and the predictions are changed for the outlying genes. Otherwise, no start site prediction is made for the ortholog set.

::DEVELOPER

Michael Wall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GMV

:: MORE INFORMATION

Citation

Genome majority vote improves gene predictions.
Wall ME, Raghavan S, Cohn JD, Dunbar J.
PLoS Comput Biol. 2011 Nov;7(11):e1002284.

GMV 1.0c-beta – Genome Map Viewer

GMV 1.0c-beta

:: DESCRIPTION

GMV (Genome Map Viewer) is a tool that compares gene order in two or more genomes and displays the results in the form of the concentric ring display of Moore et al.(1995) and Gale and Devos (1998). This display shows the relative positions of linkage blocks in a set of species, where these blocks have been proposed on the basis of conservation of gene order across the species being examined. In cereals these blocks are often based on rice.

::DEVELOPER

 DICKS COMPUTATIONAL BIOLOGY GROUP

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

  GMV

:: MORE INFORMATION