DOMAINNR(1e)

💖 DOMAINNR 💖

okay so bestie, welcome to the DOMAINNR(1e) page, straight out of the EMBOSS Manual for Debian 🎀 she's a little utility, she's lowkey a baddie, and she's here to clean up your domain files. let's get into it ✨

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✨ NAME ✨

domainnr — Removes redundant domains from a DCF file. 💅

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🌸 SYNOPSIS 🌸

domainnr -dcfinfile infile [-datafile matrixf] -retain toggle -node list
         -mode list -threshold float -threshlow float -threshup float
         [-gapopen float] [-gapextend float] -dcfoutfile outfile
         -redoutfile outfile -logfile outfile

domainnr -help

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🦋 DESCRIPTION 🦋

so domainnr is a command line program from EMBOSS — that's "the European Molecular Biology Open Software Suite" if you're new here, hi, welcome 🫶 — and she belongs to the "Utils:Database creation" command group(s). no cap.

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💅 OPTIONS 💅

🍓 Input section

• -dcfinfile infile — this one's the name of the DCF file (domain classification file), and it's the input. a 'domain classification file' holds classification and other data for domains from SCOP or CATH, all in DCF format (EMBL-like, iykyk). these files get generated by using SCOPPARSE and CATHPARSE, and you can add domain sequence info to the file by using DOMAINSEQS. 👑
• -datafile matrixf — specifies the residue substitution matrix, which is used for sequence comparison. Default value: EBLOSUM62. slay.
• -retain toggle — this one's a vibe check on whether you wanna write the redundant domains out to a separate file. if you pick this option, the redundant domains go to a separate output file. Default value: N. 🙈

⭐ Required section

• -node list — specifies the node for redundancy removal. the way that redundancy can be removed at any specified node in the SCOP or CATH hierarchies... iconic. for example, by selecting 'Class', entries belonging to the same Class will be non-redundant. Default value: 1. ✨
• -mode list — specifies whether to remove redundancy at a single threshold % sequence similarity, or to remove redundancy outside a range of acceptable threshold % similarity. all permutations of pair-wise sequence alignments are calculated for each domain family in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm. redundant sequences get removed in one of two modes, as follows:
  • (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. 💀 shortest one gets voted off the island, fr fr.

• -threshold float — specifies the % sequence identity redundancy threshold, which determines the redundancy calculation. if a pair of proteins achieve greater than this threshold, the shortest sequence is discarded. Default value: 95.0. 🔥
• -threshlow float — specifies the % sequence identity redundancy threshold, which determines 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.
• -threshup float — specifies the % sequence identity redundancy threshold, which determines 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: 90.0.

🧚 Additional section

• -gapopen float — specifies the gap insertion penalty. this 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: 10. 💜
• -gapextend float — specifies the gap extension penalty. this is added to the standard gap penalty for each base or residue in the gap, and that's how long gaps are penalized. usually you'll 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. 🌈

🌸 Advanced section

okay bestie there is literally nothing listed under Advanced here. not a single option. it's giving minimalist. we move on. 💅

👑 Output section

• -dcfoutfile outfile — specifies the name of the non-redundant DCF file (domain classification file) — that's the output. a 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). the files are generated by using SCOPPARSE and CATHPARSE, and domain sequence information can be added to the file by using DOMAINSEQS. Default value: test.scop. ✨
• -redoutfile outfile — specifies the name of the DCF file (domain classification file) for the redundant sequences — also output. a 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). the files are generated by using SCOPPARSE and CATHPARSE, and domain sequence information can be added to the file by using DOMAINSEQS.
• -logfile outfile — specifies the name of the log file for the build. the log file contains messages about any errors arising while domainnr ran. Default value: domainnr.log. 🫶

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💀 BUGS 💀

found a bug? not the vibe, but okay. 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). 🐛

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🔥 SEE ALSO 🔥

domainnr is fully documented via the tfm(1) system. so if you want the whole lore, that's where it lives, bestie. 📚

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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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and that's the whole page, no notes 🫶 this lil number came from DOMAINATRIX version 0.1.0+20100721, dated 08/11/2010, and yeah it's the DOMAINNR(1e) page you just read. stay non-redundant, bestie 💅✨🌸