NEEDLE(1e)

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

✨ NAME ✨

okay so bestie, welcome to NEEDLE(1e) — this is the EMBOSS Manual for Debian version, and the vibe is: needle does Needleman-Wunsch global alignment of two sequences. global. the whole thing. no crumbs left behind. 💅

🌸 SYNOPSIS 🌸

needle -asequence sequence -bsequence seqall [-datafile matrixf]
       -gapopen float -gapextend float [-endweight boolean]
       [-endopen float] [-endextend float] -brief boolean -outfile align

needle -help

like. that's the whole summoning ritual. needle -help if you're lost, which, no judgement, we've all been there 🫶

🦋 DESCRIPTION 🦋

needle is a command line program from EMBOSS — aka “the European Molecular Biology Open Software Suite” — and she is that girl. she's part of the "Alignment:Global" command group(s), so you already know she's aligned.

💖 OPTIONS 💖

🎀 Input section 🎀

  • -asequence sequence — your first sequence goes here. main character #1.
  • -bsequence seqall — and here's your second sequence. main character #2. the alignment is literally their meet-cute.
  • -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 your EMBOSS installation. no cap. 📁

🔥 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 you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Default value: @($(acdprotein)? 10.0 : 10.0 )
  • -gapextend float — the gap extension penalty is added to the standard gap penalty for each base or residue in the gap. this is how long gaps are penalized. usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. an exception is where one or both sequences are single reads with possible sequencing errors, in which case you would expect many single base gaps. you can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. Default value: @($(acdprotein)? 0.5 : 0.5 ) ✨

🌈 Additional section 🌈

  • -endweight boolean — Default value: N
  • -endopen float — the end gap open penalty is the score taken away when an end gap is created. the best value depends on the choice of comparison matrix. the default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Default value: @($(acdprotein)? 10.0 : 10.0 )
  • -endextend float — the end gap extension penalty is added to the end gap penalty for each base or residue in the end gap. this is how long end gaps are penalized. Default value: @($(acdprotein)? 0.5 : 0.5 )

👑 Output section 👑

  • -brief boolean — brief identity and similarity. Default value: Y
  • -outfile align — where your beautiful little alignment lands. 💾

💀 BUGS 💀

not me having to tell you this, but 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). they want to hear from you fr fr 🙈

🌟 SEE ALSO 🌟

needle is fully documented via the tfm(1) system. go read it, iykyk 📖

🫶 AUTHOR 🫶

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

  • Wrote the script used to autogenerate this manual page. iconic behaviour 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 page, bestie!! this little love letter is EMBOSS 6.4.0, dated 05/11/2012, filed under NEEDLE(1e) — go align something gorgeous 🌸💅✨

📦 where this page comes from