Proteinortho Helper

The resulting proteinortho command (replace proteinortho with 'perl proteinortho6.pl' for a local execution):

proteinortho

Main parameters

-step

Do all steps (1-3)

1: Build Databases

2: All versus all blast

3: Clustering

-project : prefix for all resulting file names

-cpus : the number of processors/ threads

-verbose : the verbosity level

Additional Flags

-selfblast : apply selfblast, detects paralogs without orthologs.

-silent : verbosity level 0

-clean : removes all database-index-files generated by the -p algorithm afterwards.

-keep : save all intermediate results (inside the folder: *proteinortho_cache/).

-force : forces the recalculation of the blast results in any case in step=2 and the rebuilding of the databases in step=1.

-desc : write description files (for NCBI FASTA input only)

-cleanblast : cleans blast-graph with proteinortho_cleanupblastgraph (either generated in step 2 or loaded in step 3)

-debug

-binpath : path to your local executables (blast, diamond, ...), e.g. /home/paul/bin/

-tmp : path to the temporary files. E.g. /tmp/ or to a proteinortho_cache_* directory of a previous run (use the -keep option).

Search options (step 1-2)

-e : evalue threshold for the search algorithm. Increasing this threshold will result in more hits (be careful of false positives).

-sim : minimal similarity threshold for additional hits. The RBH (reciprocal best hit blast graph) only contains the best/maximal hits between two species, this corresponds to -sim=1. With 0.95 the best 5% are taken (adaptive RBH).

-identity : min. percent identity of best blast hits in %

-cov : min. coverage of best blast alignments in %

-subparaBlast : additional parameters for the search tool(-p). Careful when changing -p, then this option may lead to errors.
''

-checkfasta : checks if the given algorithm (-p) can process the input fasta file.

-identical : only return entries that are 100% identical.

-range : maximal length difference for any blast hit. e.g. 0 = filter for hits between proteins of same length. -1=disabled

-isoform : Enables the isoform processing: Treat all isoforms as one protein(family) and choose the best blast score adaptively for each comparison. E.g. Let I1 and I2 two isoforms, I1 reciprocally matches A and I2 B but no other hits are found: with this option the output is A-I-B (results of I1 and I2 are merged)

disabled

ncbi (Different proteins have the same gene id. The word isoform is mandatory!)

uniprot (Isoforms are specified in uniprot style using the '*_additional.fa' files, just add these files to the analysis)

trinity (Isoforms are given in the trinity ids TRINITY_DN1000_c115_g5_i1 -> isoform 1)

Synteny options (optional, step 2)

-synteny : activate PoFF extension to separate similar by contextual adjacencies. Requires a .gff for each .fasta in the same directory with same names.

-dups : number of reiterations for adjacencies heuristic, to determine duplicated regions

-cs : Size of a maximum common substring (MCS) for adjacency matches

-alpha : weight of adjacencies vs. sequence similarity

Clustering options (step 3)

-conn : minimal required algebraic connectivity for each connected component/group. This is the main parameter for the clustering algorithm. The higher this value, the more splits are made.

-purity : avoid spurious graph assignments by increasing this value

-minspecies : minimal number of genes per species for each group. If a group is found with up to (minspecies) genes/species, it wont be split again (regardless of the connectivity). A value of 0 is always satisfied.

-subparaCuster : additional parameters for the clustering algorithm
''

Additional Flags

-nograph : do not generate the pairwise orthology relations file (*-graph).

-singles : report groups only containing a single genes without any hits.

-xml : do generate an orthoXML file (www.orthoxml.org). You can also use proteinortho2xml.pl.

-core : stop clustering if a split would result in groups that do not span across all species of the inital connected component. Overrules the -conn threshold.

-coreMinSpecies : sets the minimal number of species for the -core option.

-coreMaxProts : sets the maximal number of proteins per species for the -core option.

Options for large compute jobs

-jobs : If you want to involve multiple machines or separate a Proteinortho run into smaller chunks, use the -jobs=M/N option. First, run 'proteinortho6.pl -steps=1 ...' to generate the indices. Then you can run 'proteinortho6.pl -steps=2 -jobs=M/N ...' to run small chunks separately. Instead of M and N numbers must be set representing the number of jobs you want to divide the run into (M) and the job division to be performed by the process. E.g. to divide a Proteinortho run into 4 jobs to run on several machines, use 'proteinortho6.pl -steps=2 -jobs=1/4', 'proteinortho6.pl -steps=2 -jobs=1/4', 'proteinortho6.pl -steps=2 -jobs=2/4', 'proteinortho6.pl -steps=2 -jobs=3/4', 'proteinortho6.pl -steps=2 -jobs=4/4'.
N = (only available for -step=2)