multi-gridsam-gopher

Generation of Orthologous Proteins from High-Throughput Estimation of Relationships

This workflow uses GOPHER to take in two protein sequence files and generate datasets of orthologous sequence alignments.

The first [seqin] sequence set is the 'queries' around which orthologous datasets are to be assembled. This is now optimised for a dataset consisting of one protein per protein-coding gene, although splice variants should be dealt with OK and treated as paralogues.

The second [orthdb] is the list of proteins from which the orthologues will be extracted. The seqin sequences are then BLASTed against the orthdb and processed to retain putative orthologues using an estimation of the phylogenetic relationships based on pairwise sequences similarities.

This version of the workflow utilises a GridSAM backend for parallelisation, currently this employs a PBS cluster in Southampton and thus access is restricted to members of the University.

More info on GOPHER: http://bioinformatics.ucd.ie/shields/software/gopher/index.html