CSB-BUILDHMM(1)

📦 version 1.2.5, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 CSB-BUILDHMM 💖

okay bestie, gather round, because we're talking about csb-buildhmm from section 1 of the manual, and it's literally the glow-up your sequence needs 🦋

✨ NAME ✨

csb-buildhmm — build an HMM from a FASTA sequence 👑

🌸 DESCRIPTION 🌸

here's the whole vibe, exactly how it ships:

usage: csb-buildhmm [-h] -q QUERY_ID [-t TK_ROOT] [-d DATABASE] [-c
       TK_CONFIG]

       [--cpu CPU] [--no-ss] [--no-pseudo] [--no-calibration]
              query

so what does it do? it builds an HMM from a FASTA sequence, periodt. and the way it does that is by being a proxy to hhblits/addss.pl and hhmake from the HHpred package 🫶

@note: assuming you have the full HHpred package installed and configured. no HHpred, no HMM, iykyk 💀

🎀 positional arguments 🎀

  • query — the input sequence (that's a FASTA or PDB file, bestie)

💅 optional arguments 💅

  • -h, --help — show this help message and exit, iconic behaviour honestly
  • -q QUERY_ID, --query-id QUERY_ID — the ID of the query, in PDB-like format (accessionCHAIN). this is what names your output files 🌈 also, if your input is a PDB file with multiple chains, CHAIN is what pulls the required chain out of the file
  • -t TK_ROOT, --tk-root TK_ROOT — path to the ToolkitRoot folder in your HHsuite setup (default=/ebio/abt1_toolkit/share/wye)
  • -d DATABASE, --database DATABASE — a custom HHblits database; if you don't define one, the toolkit's unirpto20 gets used instead
  • -c TK_CONFIG, --tk-config TK_CONFIG — path to a folder containing custom HHsuite configs (e.g. HHPaths.pm) (default=.)
  • --cpu CPU — maximum degree of parallelism (default=1)
  • --no-ss — do not include secondary structure (default=False)
  • --no-pseudo — do not add emission and transition pseudocounts (default=False)
  • --no-calibration — do not calibrate the profile (default=False)

👑 AUTHOR 👑

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

okay that's the whole page, you ate it 💖 this was csb-buildhmm version 1.2.5, dated November 2017, and honestly? still serving. mwah 🎀✨

📦 where this page comes from