DIFFSEQ(1e)

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

💖 DIFFSEQ 💖 (that's DIFFSEQ(1e) bestie, from the EMBOSS Manual for Debian)

okay so. sit down. hydrate. because we're about to compare two sequences and it's gonna be so good.

✨ NAME ✨

diffseq — compare and report features of two similar sequences 🦋

✨ SYNOPSIS ✨

diffseq -asequence sequence -bsequence sequence -wordsize integer
        [-globaldifferences boolean] -outfile report -aoutfeat featout
        -boutfeat featout

diffseq -help

✨ DESCRIPTION ✨

diffseq is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It's part of the "Alignment:Differences" command group(s). she's aligned, she's diffing, she's serving. 💅

✨ OPTIONS ✨

🌸 Input section

  • -asequence sequence — your first sequence goes here 🫶
  • -bsequence sequence — and this is where the second one lives ✨

🌸 Required section

  • -wordsize integer — so here's the tea: the similar regions between the two sequences get found by building a hash table of 'wordsize'-length subsequences. 10 is a reasonable default, fr fr. Making this value bigger (like 20?) might speed the program up a little, but the tradeoff is that any two differences within 'wordsize' of each other will get grouped into one single region of difference. Making it smaller instead (like 4?) sharpens the resolution of nearby differences — but the program will go much slower. 😭 Default value: 10

🌸 Additional section

  • -globaldifferences boolean — okay so normally this program finds regions of identity that are at least as long as the specified word-size, and then reports the regions of difference between those matching regions. That works great and it's what most people want when they're working with long overlapping nucleic acid sequences — because you're usually not interested in the non-overlapping ends of those sequences. BUT. If you've got protein sequences or short RNA sequences, you will care about differences at the very ends 👀. If this option is set to be true, then those end differences get reported too. Default value: N

🌸 Output section

  • -outfile report — the report goes here 💖
  • -aoutfeat featout — file for output of the first sequence's features. Default value: $(asequence.name).diffgff
  • -boutfeat featout — file for output of the second sequence's features. Default value: $(bsequence.name).diffgff

✨ BUGS ✨

Found a bug? 😭 not the vibe, but okay, report it to the Debian Bug Tracking system at http://bugs.debian.org/emboss, or go straight to the EMBOSS developers at http://sourceforge.net/tracker/?group_id=93650&atid=605031.

✨ SEE ALSO ✨

diffseq 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. iconic behavior honestly 👑

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 thing bestie!! 🌈 this was EMBOSS 6.4.0, dated 05/11/2012, and it's DIFFSEQ(1e) — go compare some sequences, you absolute main character 🫶✨💜

📦 where this page comes from