PhyloPat 52 – Phylogenetic Pattern analysis of Eukaryotic Genes

PhyloPat 52

:: DESCRIPTION

PhyloPat (Phylogenetic Patterns) is an easy-to-use webserver, which can be used to query the orthologies of all complete genomes within the EnsMart database using phylogenetic patterns. This enables the determination of sets of genes that occur only in certain evolutionary branches or even single species.

::DEVELOPER

PhyloPat team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

PhyloPat: phylogenetic pattern analysis of eukaryotic genes.
Hulsen T, de Vlieg J, Groenen PM.
BMC Bioinformatics. 2006 Sep 1;7:398.

PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood.
Hulsen T, Groenen PM, de Vlieg J, Alkema W.
Nucleic Acids Res. 2009 Jan;37(Database issue):D731-7. doi: 10.1093/nar/gkn645. Epub 2008 Oct 2.

EGPred – Eukaryotic Gene Prediction Server

EGPred

:: DESCRIPTION

EGPred allows to predict gene (protein coding regions) in eukaryote genomes that includes introns and exons, using similarity aided (double) and consensus Ab Intion methods.

::DEVELOPER

EGPred Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Issac, B and Raghava, G P S (2004),
EGPred: Prediction of Eukaryotic Genes Using ab initio Methods After Combining With Sequence Similarity Approaches,
Genome Res 14, 1756-1766.

EVIGAN 1.0 – Eukaryotic Gene Predictor

EVIGAN 1.0

:: DESCRIPTION

Evigan is an automated gene annotation program for eukaryotic genomes, employing probabilistic inference to integrate multiple sources of gene evidence. The probabilistic model is a dynamic Bayes network whose parameters are adjusted to maximize the probability of observed evidence. Consensus gene predictions are then derived by maximum likelihood decoding, yielding n-best models (with probabilities for each).

::DEVELOPER

Structured Learning at Penn

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Evigan

:: MORE INFORMATION

Citation

Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction.
Liu Q, Mackey AJ, Roos DS, Pereira FC.
Bioinformatics. 2008 Mar 1;24(5):597-605. Epub 2008 Jan 10.