Tag: Paralog

SPOCS 1.0.10 – Graph-based Ortholog/Paralog Prediction tool

SPOCS 1.0.10

:: DESCRIPTION

SPOCS (Species Paralogy and Orthology Clique Solver) is a graph-based ortholog/paralog prediction tool that will predict orthologs and paralogs given a set of prokaryotic proteomes (the set of proteins encoded by a genome). The software will take a set of protein fasta files (one per species genome), and an optional additional fasta to serve as an outgroup (a species that should be more distantly related to the species of interest than any of the species of interest are to each other).

::DEVELOPER

Computational Biology & Bioinformatics ,Pacific Northwest National Laboratory

:: SCREENSHOTS

SPOCS

:: REQUIREMENTS

  • Linux/ MacOsX
  • C++ Compiler
  • NCBI BLAST

:: DOWNLOAD

 SPOCS

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 15;29(20):2641-2. doi: 10.1093/bioinformatics/btt454.
SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes.
Curtis DS, Phillips AR, Callister SJ, Conlan S, McCue LA.

orthoFind – Obtain Orthologs and Paralogs of Protein Sequence

orthoFind

:: DESCRIPTION

orthoFind searchs for homologous and orthologous proteins at a genomics level. It allows a quick search given one or more query sequences, and it can search either Swiss-Prot, a collection of reference proteomes, or user datasets. These results are accompanied with a simple functional annotation, including a study of their domain architecture.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2015 Dec 1;10(12):e0143906. doi: 10.1371/journal.pone.0143906.
orthoFind Facilitates the Discovery of Homologous and Orthologous Proteins.
Mier P, Andrade-Navarro MA, Pérez-Pulido AJ.