PFSEARCHV3(1)

📦 version 3.2.12, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 PFSEARCHV3(1) 💖

okay bestie, gather round, because this is pfsearchV3 — the version 3 glow-up of pfsearch, and she lives in the User Commands section of the manual, so you know she's a real one ✨

🌸 NAME 🌸

pfsearchV3 — search protein and DNA generalized profiles (version 3)

🎀 SYNOPSIS 🎀

pfsearch [options] profile database

like, that's the whole vibe. a profile and a database, plus whatever options you feel like serving 💅

🦋 DESCRIPTION 🦋

okay so here's the tea: you build protein and DNA generalized profiles, and then you use them to scan and align sequences, and also to search databases. that's it, that's the whole job. main character energy fr fr 👑

✨ OPTIONS ✨

💜 Profile

  • --level, -l — level to use for cutoff
  • --mode, -m — mode to use for normalization

🍓 Database

  • --create-index-database, -c — output indices to given file
  • --use-index-database, -i — use indices stored in given file

🔥 Heuristic

  • --cutoff, -C — heuristic cutoff value
  • --dump-heuristic-scores, -A — only print heuristic scores to stdout
  • --dump-heuristic-sequences, -D — dump passed heuristic sequences

🧚 Filter

  • --dump-filter-scores, -a — only print filter scores to stdout
  • --dump-filter-sequences, -d — dump passed heuristic and filter sequences

⭐ Optimizations

  • --sse2, -s — enforces SSE 2 only instruction set
  • --nthreads, -t — max number of threads to use
  • --max-heuristic-nthreads, -T — max number of threads to use for heuristic phase only. (IO bounds)
  • --no-affinity, -f — disable CPU affinity file
  • --thread-affinity, -M — file containing thread mask, one row for one thread
  • --no-shared-core, -k — Prevent core resource sharing
  • --split, -b — if both SSE 2 & 4.1 are available, split half-half using linked resources

🌈 Printing output

  • --output-method, -o — printing output method
    • == 0 replicates the pfseach output without options (DEFAULT)
    • == 1 simple output
    • == 2 replicates pfsearch -lxz output
    • == 3 replicates pfscan -lxz output
    • == 4 tsv output (single line tab delimited)
  • --output-length, -W — maximum number of column for sequence output printing

🙈 Other

  • --verbose, -v — verbose on stderr
  • --help, -h — output command help

👑 AUTHOR 👑

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

not me getting emotional over a manpage 😭 anyway that's the whole page, no cap, every single flag accounted for 🫶

pfsearchV3 version 3, dated March 2017 — mwah, slay, periodt 💅✨🎀

📦 where this page comes from