SKIPREDUNDANT(1e)

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

💖 SKIPREDUNDANT 💖

okay bestie, gather round, because this is skipredundant — a lil command line program from the EMBOSS suite ("the European Molecular Biology Open Software Suite", yes that's the whole vibe) and it lives in the "Edit"</> command group(s). its whole job? remove redundant sequences from an input set. that's it, that's the girl. ✨

✨ SYNOPSIS ✨

skipredundant -feature toggle -sequences seqset [-datafile matrixf]
              -mode list -threshold float -minthreshold float
              -maxthreshold float -gapopen float -gapextend float
              -outseq seqoutall -redundantoutseq seqoutall

skipredundant -help

like, the second one is just the cry-for-help line, she's got you 🫶

🌸 DESCRIPTION 🌸

skipredundant is a command line program from EMBOSS — and no cap, it's part of the "Edit"</> command group(s). she reads a set of sequences, finds the ones that are basically saying the same thing twice, and ghosts the extras. iconic behaviour honestly 💅

🎀 OPTIONS 🎀

Input section 📥

  • -feature toggle — if you set this, the sequence feature information will be retained. so all your lil annotations stay, bestie ✨
  • -sequences seqset — this is your input sequence set. no description beyond that, she is what she is 🦋
  • -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. so if you can't find them, that's where they're hiding 🍓

Required section ⭐

these ones are not optional, bestie. she needs them. periodt.
  • -mode list — this tells her whether to remove redundancy at a single threshold percentage sequence similarity, or to remove redundancy outside a range of acceptable threshold percentage similarity. all permutations of pair-wise sequence alignments get calculated for each set of input sequences in turn, using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm. redundant sequences are then removed in one of two modes, and here they are:
    • (i) if a pair of proteins achieve greater than a threshold percentage sequence similarity (you specify it) — the shortest sequence is discarded.
    • (ii) if a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (you specify it) — the shortest sequence is discarded.

Default value: 1 👑

  • -threshold float — this one sets the percentage sequence identity redundancy threshold. that threshold is what drives the redundancy calculation. if a pair of proteins achieve greater than this threshold, the shortest sequence is discarded. Default value: 95.0 💖
  • -minthreshold float — this sets the percentage sequence identity redundancy threshold (lower limit). same deal, it drives the redundancy calculation. if a pair of proteins have a percentage sequence similarity that lies outside an acceptable range, the shortest sequence is discarded. Default value: 30.0 🌸
  • -maxthreshold float — and this sets the percentage sequence identity redundancy threshold (upper limit). again, it's the redundancy calculation's whole personality. if a pair of proteins have a percentage sequence similarity that lies outside an acceptable range, the shortest sequence is discarded. Default value: 90.0 🌈
  • -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 assumes you're using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Default value: @($(acdprotein)? 10.0 : 10.0 ) 💅
  • -gapextend float — the gap extension penalty is added to the standard gap penalty for each base or residue in the gap. this is how long gaps are penalized. usually you'd expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. the exception? when one or both sequences are single reads with possible sequencing errors — then you'd expect many single base gaps. you can get that result by setting the gap open penalty to zero (or very low) and letting the gap extension penalty control gap scoring. Default value: @($(acdprotein)? 0.5 : 0.5 ) 🧚

Advanced section 🔮

she's empty, bestie. not a single thing in here. just vibes ✨

Output section 📤

  • -outseq seqoutall — where the output goes. that's the whole note 💜
  • -redundantoutseq seqoutall — where the redundant ones go. also the whole note 🎀

💀 BUGS 💀

found a bug? report it, don't just suffer in silence. 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). 🫶

👑 SEE ALSO 👑

skipredundant is fully documented via the tfm(1) system. go read her sister page, iykyk 💖

🌟 AUTHOR 🌟

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

  • Wrote the script used to autogenerate this manual page. yes, a script wrote this. we're all just out here living our lives 🙈

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. no cap, that's the whole license situation ✨

okay that's the page!! she's EMBOSS 6.4.0, dated 05/11/2012, and yeah — the footer says SKIPREDUNDANT(1e) because she's a section 1e manual page, main character energy to the very end 👑💖 bye bestie, go dedupe those sequences 🧬✨

📦 where this page comes from