This is the command proteinortho5 that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
proteinortho5 - orthology detection tool
SYNOPSIS
proteinortho5 [OPTIONS] FASTA1 FASTA2 [FASTA...]
DESCRIPTION
Proteinortho is a stand-alone tool that is geared towards large datasets and makes use of
distributed computing techniques when run on multi-core hardware. It implements an
extended version of the reciprocal best alignment heuristic. Proteinortho was applied to
compute orthologous proteins in the complete set of all 717 eubacterial genomes available
at NCBI at the beginning of 2009. Authors succeeded identifying thirty proteins present in
99% of all bacterial proteomes.
OPTIONS
-e= E-value for blast [default: 1e-05]
-p= blast program {blastn|blastp|blastn+|blastp+} [default: blastp+]
-project=
prefix for all result file names [default: myproject]
-synteny
activate PoFF extension to separate similar sequences by contextual adjacencies
(requires .gff for each .fasta)
-dups= PoFF: number of reiterations for adjacencies heuristic, to determine duplicated
regions (default: 0)
-cs= PoFF: Size of a maximum common substring (MCS) for adjacency matches (default: 3)
-alpha=
PoFF: weight of adjacencies vs. sequence similarity (default: 0.5)
-desc write description files (for NCBI FASTA input only)
-keep stores temporary blast results for reuse
-force forces recalculation of blast results in any case
-cpus= number of processors to use [default: auto]
-selfblast
apply selfblast, detects paralogs without orthologs
-singles
report singleton genes without any hit
-identity=
min. percent identity of best blast hits [default: 25]
-cov= min. coverage of best blast alignments in % [default: 50]
-conn= min. algebraic connectivity [default: 0.1]
-sim= min. similarity for additional hits (0..1) [default: 0.95]
-step= 1 -> generate indices 2 -> run blast (and ff-adj, if -synteny is set) 3 ->
clustering 0 -> all (default)
-blastpath=
path to your local blast (if not installed globally)
-verbose
keeps you informed about the progress
-clean remove all unnecessary files after processing
-graph generate .graph files (pairwise orthology relations)
-debug gives detailed information for bug tracking
More specific blast parameters can be defined by
-blastParameters='[parameters]' (e.g. -blastParameters='-seg no')
In case jobs should be distributed onto several machines, use
-startat= File number to start with (default: 0)
-stopat= File number to end with (default: -1)
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