MATCHER(1e)

💖 MATCHER(1e) 💖

okay bestie, welcome to the EMBOSS Manual for Debian page for matcher — yes the (1e) is part of the whole vibe, don't question it ✨

---

✨ NAME ✨

matcher — Waterman-Eggert local alignment of two sequences 🧬💅

---

🌸 SYNOPSIS 🌸

matcher -asequence sequence -bsequence sequence [-datafile matrix]
        [-alternatives integer] [-gapopen integer] [-gapextend integer]
        -outfile align

matcher -help

like, that's the whole summoning ritual. -asequence and -bsequence and -outfile are the non-negotiables, the rest are optional little accessories 🎀

---

🦋 DESCRIPTION 🦋

matcher is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It's part of the "Alignment:Local" command group(s). no cap, that's literally the group it lives in 🫶

---

👑 OPTIONS 👑

🍓 Input section 🍓

• -asequence sequence — the first sequence you're feeding in. go off.
• -bsequence sequence — and this is the second one. the matchup we've all been waiting for 💖
• -datafile matrix — This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. iykyk, the vibes matrix 📊✨

🌈 Additional section 🌈

• -alternatives integer — This sets the number of alternative matches output. By default only the highest scoring alignment is shown. A value of 2 gives you other reasonable alignments. In some cases, for example multidomain proteins of cDNA and genomic DNA comparisons, there may be other interesting and significant alignments. Default value: 1. so like, 1 is the main character, 2 is when you want the supporting cast too 👑
• -gapopen integer — The gap penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value of 14 assumes you are using the EBLOSUM62 matrix for protein sequences, or a value of 16 and the EDNAFULL matrix for nucleotide sequences. Default value: @($(acdprotein)? 14 : 16) — yes that's literally the default expression, copy it exactly bestie, don't be cute with it 💀
• -gapextend integer — The gap length, or gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap penalty to zero (or very low) and using the gap extension penalty to control gap scoring. Default value: @($(acdprotein)? 4 : 4). gap open = the drama, gap extend = how long the drama drags on 😭

💜 Output section 💜

• -outfile align — where the alignment goes. required, no skipping, periodt ✨

---

💀 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). not me telling you where to snitch on the bugs 🙈 but fr fr, they wanna know.

---

⭐ SEE ALSO ⭐

matcher is fully documented via the tfm(1) system. that's the lore, go read it 📚

---

🎀 AUTHOR 🎀

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

• Wrote the script used to autogenerate this manual page. iconic honestly, a script doing the writing for them, main character energy 👑

---

💅 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. slay, same terms, no extra drama 🌸

---

and that's the whole page bestie!! this came to you courtesy of EMBOSS 6.4.0, dated 05/11/2012, and the MATCHER(1e) header up top 💖 mwah, go align something gorgeous ✨🦋