WORDFINDER(1e)

💖 WORDFINDER(1e) — the EMBOSS Manual for Debian edition 💖

okay bestie, sit down, hydrate, because we're about to talk about wordfinder, a lil command line program from the EMBOSS suite (that's "the European Molecular Biology Open Software Suite", and yes the acronym is doing the most ✨). It lives in the "Alignment:Local" command group(s), so if you're browsing the group list looking for it, that's where it's at 🫶

---

✨ NAME ✨

wordfinder — match large sequences against one or more other sequences 🧬

---

🌸 SYNOPSIS 🌸

wordfinder -asequence seqset -bsequence seqall [-datafile matrixf]
           -gapopen float -gapextend float [-width integer]
           [-wordlen integer] [-limitmatch integer]
           [-limitalign integer] [-lowmatch integer] [-lowalign integer]
           -outfile align [-errorfile outfile]

wordfinder -help

---

🦋 DESCRIPTION 🦋

wordfinder is a command line program from EMBOSS (the European Molecular Biology Open Software Suite, iconic behavior honestly). It's part of the "Alignment:Local" command group(s). It matches large sequences against one or more other sequences. That's the whole vibe. Periodt 💅

---

🎀 OPTIONS 🎀

Input section 🌈

• -asequence seqset — your first sequence input (a set of sequences, no cap).
• -bsequence seqall — the other sequence(s) you're matching against.
• -datafile matrixf — the scoring matrix file used when comparing sequences. By default it's the file EBLOSUM62 (for proteins) or the file EDNAFULL (for nucleic sequences). You'll find these files hanging out in the data directory of your EMBOSS installation 🗂️

Required section 🔥

• -gapopen float — gap open penalty. Default value: @($(acdprotein)? 30.0 : 30.0)
• -gapextend float — gap extension penalty. Default value: @($(acdprotein)? 1.5 : 1.5)

these two are required, bestie. no skipping, the program literally needs them.

Additional section 🍓

• -width integer — Default value: 16
• -wordlen integer — Default value: 6
• -limitmatch integer
• -limitalign integer
• -lowmatch integer
• -lowalign integer

Output section 💜

• -outfile align — where the alignment goes.
• -errorfile outfile — Error file to be written to. Default value: wordfinder.error

---

💀 BUGS 💀

Found something cursed? Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or you can go straight to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). They wanna hear it, fr fr 🐛

---

👑 SEE ALSO 👑

wordfinder 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. (not me tho, i just did the vibes 💅)

---

🌟 COPYRIGHT 🌟

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 — that's the source, version and date bestie, mwah, drink some water and go match some sequences 🫶💖✨