PROTEINORTHO6(1)

🌸 PROTEINORTHO6 — orthology detection tool 🌸

okay bestie, sit down, hydrate, because today we're learning proteinortho6 from the User Commands manual, and honestly? it's giving icon behavior. 💅

✨ NAME ✨

proteinortho6 — orthology detection tool 🧬

🦋 SYNOPSIS 🦋

proteinortho6 [OPTIONS] FASTA1 FASTA2 [FASTA...]

👑 DESCRIPTION 👑

Proteinortho is a stand-alone tool, and no because it's literally built for the big girl datasets 💅 — it uses distributed computing techniques when you run it on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic, which, yes, sounds like a lot, but trust the process.

The way it was applied to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009?? iconic. And the authors succeeded identifying thirty proteins present in 99% of all bacterial proteomes. no cap. 🫶

🎀 OPTIONS 🎀

• -e= — E-value for blast [default: 1e-05]
• -p= — blast program, and you get to pick from {blastp+|blastn+|tblastx+|diamond|usearch|ublast|lastp|lastn|rapsearch|topaz|blatp|blatn|mmseqsp|mmseqsn} [default: diamond] 💎
• -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) 🔥
• -binpath= — path to your local blast/diamond/... (if not installed globally)
• -verbose — keeps you informed about the progress 🗣️
• -clean — remove all unnecessary files after processing 🧹
• -debug — gives detailed information for bug tracking 🐛

💖 more specific blast params, bestie

More specific blast parameters can be defined by

-subparaBLAST='[parameters]' (e.g. -subparaBLAST='-seg no')

🌈 distributing jobs across machines

In case jobs should be distributed onto several machines, use

-jobs=M/N

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. 🚀

fr fr, don't skip the index step — -steps=1 first, always. the whole chunking thing depends on it.

that's the whole page, bestie 💖 this was proteinortho6 version 6.0.6, from November 2015, living its best life in the User Commands section of the manual. go forth and cluster, you absolute icon 👑✨