WATER(1e)

📦 version 6.6.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💧 NAME 💧

water — Smith-Waterman local alignment of sequences. bestie. it aligns ur sequences. locally. that's the whole vibe.

✨ SYNOPSIS ✨

water -asequence sequence -bsequence seqall [-datafile matrixf]
      -gapopen float -gapextend float -brief boolean -outfile align

water -help

🦋 DESCRIPTION 🦋

okay so water is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). no cap, that's the full name, it's iconic.

it lives in the "Alignment:Local" command group(s), which is exactly where u'd expect a local aligner to be hanging out. main character energy fr fr 💅

🎀 OPTIONS 🎀

💖 Input section 💖

  • -asequence sequence — ur first sequence goes here, bestie.
  • -bsequence seqall — and here's the second one. the one ur comparing it to.
  • -datafile matrixf — this is the scoring matrix file used when comparing sequences. by default it's the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). these files are found in the 'data' directory of the EMBOSS installation. so like, that's where they live. 🏠

🌸 Required section 🌸

  • -gapopen float — the gap open penalty is the score taken away when a gap is created. the best value depends on the choice of comparison matrix. the default value assumes u are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Default value: @($(acdprotein)? 10.0 : 10.0)
  • -gapextend float — the gap extension penalty is added to the standard gap penalty for each base or residue in the gap. this is how long gaps are penalized. usually u will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. an exception is where one or both sequences are single reads with possible sequencing errors, in which case u would expect many single base gaps. u can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. Default value: @($(acdprotein)? 0.5 : 0.5)
not me explaining gap penalties like a group project 💀 but seriously, gap open = how much it costs to START a gap, gap extend = how much it costs to KEEP GOING. that's the whole thing.

👑 Output section 👑

  • -brief boolean — Brief identity and similarity. Default value: Y
  • -outfile align — where ur beautiful alignment gets written, queen. ✨

💀 BUGS 💀

bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

if u find a bug, pls report it, don't just suffer in silence. we don't do that here 🫶

🌈 SEE ALSO 🌈

water is fully documented via the tfm(1) system. iykyk.

💜 AUTHOR 💜

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

  • Wrote the script used to autogenerate this manual page. (so this whole page was built by a script, and now it's been built again, but make it cute. the pipeline is giving ✨automation✨)

this manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. it can be redistributed under the same terms as EMBOSS itself.

EMBOSS 6.4.0 · 05/11/2012 — ok that's the version and the date, bestie, and that's the whole page! go align something slay 💅🦋

📦 where this page comes from