SEQNR(1e)

💖 SEQNR(1e) — the EMBOSS manual for Debian, but make it a group chat 💖

okay bestie, sit down, hydrate, and let me tell you about seqnr — a lil command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). She lives in the "Utils:Database creation" command group(s), and honestly? she's the friend who quietly deletes your duplicate screenshots. Iconic behavior.

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✨ NAME ✨

seqnr — Removes redundancy from DHF files. 🧹✨

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🌸 SYNOPSIS 🌸

seqnr -dhfinpath dirlist -dosing toggle -singletsdir directory
      -dosets toggle -insetsdir directory [-matrix matrixf] -mode list
      -thresh float -threshlow float -threshup float [-gapopen float]
      [-gapextend float] -dhfoutdir outdir -dored toggle
      -redoutdir outdir -logfile outfile

seqnr -help

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🦋 DESCRIPTION 🦋

seqnr is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Utils:Database creation" command group(s).

That's the whole vibe. She deduplicates. She ships. 💅

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🎀 OPTIONS 🎀

💜 Input section

• -dhfinpath dirlist — tells her where the DHF files (domain hits files) are, and yes those are the input ones. So what's a 'domain hits file', you ask? It's a file with database hits (sequences) plus domain classification info, in the DHF format (FASTA or EMBL-like). Those hits are relatives to a SCOP or CATH family and they come from searching a sequence database. Files with hits retrieved by PSIBLAST are generated by using SEQSEARCH. Default value: ./
• -dosing toggle — do we use singlet sequences (e.g. DHF files) to filter the input? Yes or no. And listen: optionally, up to two further directories of sequences may be read — they get considered in the redundancy calculation but they never appear in the output files. Sneaky little background characters. Default value: Y
• -singletsdir directory — where the singlet filter sequences (e.g. DHF files) live (input). Again, a 'domain hits file' holds database hits (sequences) with domain classification info, in DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and come from a search of a sequence database. Files with PSIBLAST-retrieved hits are generated by using SEQSEARCH. Default value: ./
• -dosets toggle — do we use sets of sequences (e.g. DHF files) to filter the input? Y or N. And yup — optionally, up to two further directories of sequences may be read; they count toward the redundancy calculation but never show up in the output files. Default value: Y
• -insetsdir directory — the location of sets of filter sequences (e.g. DAF files) (input). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family, in clustal format, annotated with domain family classification info. Files generated with SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only — and those alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Default value: ./
• -matrix matrixf — the residue substitution matrix used for sequence comparison. Default value: EBLOSUM62

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⭐ Required section

• -mode list — do we remove redundancy at a single threshold % sequence similarity, or remove redundancy outside a range of acceptable threshold % similarity? All permutations of pair-wise sequence alignments are calculated for each set of input sequences in turn, using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm. Redundant sequences get removed in one of two modes, like this:
  • (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded.
  • (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded.

Default value: 1

• -thresh float — the % sequence identity redundancy threshold. This threshold is what drives the redundancy calculation: if a pair of proteins achieve greater than this threshold, the shortest sequence gets discarded. Default value: 95.0
• -threshlow float — the % sequence identity redundancy threshold (lower limit). Same deal — this threshold determines the redundancy calculation, and 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
• -threshup float — the % sequence identity redundancy threshold (upper limit). The threshold determines the redundancy calculation, and if a pair of proteins have a percentage sequence similarity outside an acceptable range, the shortest sequence is discarded. Default value: 90.0

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🌈 Additional section

• -gapopen float — the gap insertion penalty. That's the score taken away when a gap is created. Best value depends on your 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: 10
• -gapextend float — the gap extension penalty. This penalty is added to the standard gap penalty for each base or residue in the gap — that's how long gaps get penalized. Usually you expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. Default value: 0.5

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🫶 Output section

• -dhfoutdir outdir — where to put the DHF files (domain hits files) of non-redundant sequences (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. Default value: ./
• -dored toggle — do we retain redundant sequences? If this option is set, a DHF file (domain hits file) of redundant sequences gets written. Default value: N
• -redoutdir outdir — where to put the DHF files (domain hits files) of redundant sequences (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. Default value: ./
• -logfile outfile — the name of the SEQNR log file (output). The log file contains messages about any errors arising while SEQNR ran. Default value: seqnr.log

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😭 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 manifesting a bug-free run for you bestie 🙈 but if it happens, the links above are your 911.

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👑 SEE ALSO 👑

seqnr is fully documented via the tfm(1) system.

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💅 AUTHOR 💅

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

• Wrote the script used to autogenerate this manual page.

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🌸 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.

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signing off, queen — this page is from DOMSEARCH 0.1.0++20100721, dated 08/11/2010, and she answers to SEQNR(1e). slay, go dedupe something 💖✨🎀