SUPERMATCHER(1e)

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

💖 SUPERMATCHER(1e) 💖

okay bestie, welcome to the supermatcher page from the EMBOSS Manual for Debian ✨ settle in, this one's about lining up big sequences and it's lowkey iconic 💅

🌸 NAME 🌸

supermatcher — calculates approximate local pair-wise alignments of larger sequences 🧬✨

🦋 SYNOPSIS 🦋

supermatcher -asequence seqall -bsequence seqset [-datafile matrixf]
             [-minscore float] -gapopen float -gapextend float
             [-width integer] [-wordlen integer] -outfile align
             [-errorfile outfile]

supermatcher -help

💜 DESCRIPTION 💜

So supermatcher is a command line program straight outta EMBOSS, aka “the European Molecular Biology Open Software Suite” 🫶 no cap. It rolls with the "Alignment:Local" command group(s), which is exactly the vibe you'd expect. 🌈

✨ OPTIONS ✨

🎀 Input section 🎀

  • -asequence seqall — your sequence input, bestie. It's a seqall type. 💖
  • -bsequence seqset — and here's the other one, a seqset. 🦋
  • -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 live in the 'data' directory of the EMBOSS installation. 📁✨
  • -minscore float — minimum alignment score to report an alignment. Below this? Not reported, periodt. 💅

👑 Required section 👑

  • -gapopen float — Default value: @($(acdprotein)? 10.0 : 10.0)
  • -gapextend float — Default value: @($(acdprotein)? 0.5 : 0.5)
these two are literally required, so don't come to the function without them 🙈

⭐ Additional section ⭐

  • -width integer — Default value: 16
  • -wordlen integer — Default value: 6

🍓 Output section 🍓

  • -outfile align — where your alignment output goes. 💖
  • -errorfile outfile — error file to be written to for failed alignments. Default value: supermatcher.error 😭 (yeah, alignments fail sometimes, it's giving realistic)

💀 BUGS 💀

Found a bug? Don't suffer in silence bestie, report it to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or go straight to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). 🫶

🔥 SEE ALSO 🔥

supermatcher is fully documented via the tfm(1) system. go read that too, iykyk 👑

🌸 AUTHOR 🌸

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

  • Wrote the script used to autogenerate this manual page. 🤖✨

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. 📜

and that's the whole page, babe 🎀 this one came from EMBOSS 6.4.0, dated 05/11/2012, and it's the SUPERMATCHER(1e) page 💖 mwah, go align something gorgeous 🌈✨

📦 where this page comes from