PLAST(1)

💅 NAME 💅

plast — Parallel Local Sequence Alignment Search Tool

🦋 DESCRIPTION 🦋

okay so bestie, say hi to plast 2.3.1 — she's the Parallel Local Sequence Alignment Search Tool and she is so good at what she does. Here's the vibe check on this exact build:

• Build date: 2016-02-09 09:47:45
• OS: Linux-4.3.0-1-amd64
• Compiler: /usr/bin/cc (5.3.1)
• Host CPU: 4 cores available

Quick note before we get into it: [*] marks a mandatory argument. Like, you have to give her that one. No [*] means it's optional and she'll cope, she's flexible like that. 🫶

✨ the options, one by one ✨

• -p [*] — Program Name, and your choices are plastp, tplastn, plastx, tplastx or plastn. Pick your fighter.
• -d [*] — Subject database file. mandatory, bestie.
• -i [*] — Query database file. also mandatory. she needs both, it's giving mutuals.
• -o — PLAST report Output File.
• -e — Expectation value.
• -n — Size of neighbourhood performing ungapped extension.
• -s — Ungapped threshold that triggers a small gapped extension.
• -g — threshold for the small gapped extension.
• -b — bandwidth for the small gapped extension.
• -a — Number of processors to use.
• -G — Cost to open a gap.
• -E — Cost to extend a gap.
• -xdrop-ungap — X dropoff value for Ungapped alignment, in bits. Passing zero invokes the default behavior, which is 20 bits.
• -X — X dropoff value for gapped alignment, in bits. Zero invokes the default behavior.
• -Z — X dropoff value for final gapped alignment, in bits. 0.0 invokes the default behavior.
• -index-threshold — Index threshold used to calculate the similarity between neighbours.
• -F — Filter query sequence.
• -M — Score matrix. Your picks are BLOSUM62 or BLOSUM50.
• -strand — strands for plastn: 'plus', 'minus' or 'both' (that last one's the default ✨).
• -r — reward for a nucleotide match (plastn).
• -q — penalty for a nucleotide mismatch (plastn).
• -force-query-order — Force queries ordering in output file.
• -max-database-size — Maximum allowed size, in bytes, for a database. If it's greater than that, the database gets segmented.
• -max-hit-per-query — Maximum hits per query. A value of 0 will dump all hits, and that's the default.
• -max-hsp-per-hit — Maximum alignments per hit. A value of 0 will dump all hits, and that's the default.
• -outfmt — Output format: 1 for tabulated (the default), 2 for extended tabulated, 4 for NCBI Blast-like.
• -strands-list — List of the strands (ex: "1,2,6") to be used when using algo using nucleotids databases.
• -optim-codon-stop — size of the allowed range between the last invalid character and the next stop codon.
• -factory-dispatcher — Factory that creates dispatcher.
• -factory-statistics — Factory that creates statistics builder.
• -factory-indexation — Factory that creates indexation builder.
• -factory-hit-ungap — Factory that creates ungap hits iterator.
• -factory-hit-smallgap — Factory that creates small gap hits iterator.
• -factory-hit-fullgap — Factory that creates full gap hits iterator.
• -factory-hit-composition — Factory that creates composition hits iterator.
• -factory-gap-result — Factory that creates gap alignments result.
• -factory-ungap-result — Factory that creates ungap alignments result.
• -splitter — Factory that creates an alignment splitter. String: 'normal' or 'banded' (default).
• -optim-filter-ungap — Optimization that filters out through ungap alignments.
• -bargraph — Display a progress bar during execution. cute and functional, we love.
• -bargraph-size — Nb of characters of the bargraph.
• -progression-file — Dump in a file the current execution percentage.
• -verbose — Display information during algorithm execution.
• -full-stats — Dump algorithm statistics.
• -stats — Dump generic statistics.
• -stats-fmt — Format of statistics: 'raw' (default) or 'xml'.
• -stats-auto — Automatic stats file creation.
• -alignment-progress — Dump in a file the growing number of ungap/ungap alignments during algorithm.
• -resources-progress — Dump in a file information about resources during algorithm.
• -plastrc — Pathname of the plast config file.
• -xmlfilter — Uri of a XML filter file.
• -seeds-use-ratio — Ratio of seeds to be used.
• -seeds-index-filter — seeds length to be used for the indexation filter.
• -complete-subject-database-stats-file — File path to the stats of the complete subject database.
• -W — size of the seeds.
• -h — help. she's got you. 🫶

📚 citing her 📚

if you use PLAST in your work, cite her properly bestie, she deserves it:

Nguyen VH, Lavenier D. (2009) PLAST: parallel local alignment search tool for database comparison. BMC Bioinformatics, vol 10, no 329.

🌸 AUTHOR 🌸

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. king behavior honestly. 👑

and that's the whole page, bestie 💖 this was plast 2.3.1, dated February 2016, and we're out. slay, stay aligned, and read your manpages. periodt. ✨🦋💅