DOMAINSEQS(1e)

DOMAINSEQS 💖

okay bestie, so this is the manual page for domainseqs, a little tool from the EMBOSS manual for Debian. Section 1e, command-line girlie. Let's get into it 🫶

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✨ NAME ✨

domainseqs — adds sequence records to a DCF file. that's it, that's the whole job 💅

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✨ SYNOPSIS ✨

domainseqs -dcfinfile infile -dpdbdir directory -getswiss toggle
           -pdbtospfile infile -datafile matrixf -gapopen float
           -gapextend float -dcfoutfile outfile -logfile outfile

domainseqs -help

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✨ DESCRIPTION ✨

domainseqs is a command line program from EMBOSS, aka "the European Molecular Biology Open Software Suite" 🌸. It's part of the "Utils:Database creation" command group(s). so it's giving builder energy, not analyser energy, and honestly? iconic 👑

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✨ OPTIONS ✨

🌸 Input section 🌸

• -dcfinfile infile — this one sets the name of the DCF file (domain classification file), and it's an input. a 'domain classification file' holds classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). these files get generated by using SCOPPARSE and CATHPARSE. and guess what, domain sequence info can be added to the file by using DOMAINSEQS — that's literally this program, full circle moment 🦋
• -dpdbdir directory — this sets the location of the domain CCF file (clean coordinate files), an input bestie. a 'clean cordinate file' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL-like). the files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected ✨. records for residue solvent accessibility and secondary structure get added to the file by using PDBPLUS. default value: ./
• -getswiss toggle — default value: N
• -pdbtospfile infile — this sets the name of the pdbcodes to swissprot indexing file. the swissprot:PDB equivalence file is generated by PDBTOSP
• -datafile matrixf — this sets the residue substitution matrix, which is used for sequence comparison. default value: EBLOSUM62

💜 Required section 💜

(no options listed here, she's just standing there, serving structure 🌈)

💜 Additional section 💜

• -gapopen float — this sets the gap insertion penalty. it's the score taken away when a gap is created 🕳️. the best value depends on the choice of comparison matrix. the default value assumes you're using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. default value: 10
• -gapextend float — this sets the gap extension penalty. it's added to the standard gap penalty for each base or residue in the gap. this is 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

🎀 Output section 🎀

• -dcfoutfile outfile — this sets the name of the DCF file (domain classification file), and this time it's an 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. domain sequence information can be added to the file by using DOMAINSEQS. default value: domainseqs.out
• -logfile outfile — this sets the name of log file for the build. the log file contains messages about any errors arising while domainseqs ran. default value: domainseqs.log

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😭 BUGS 😭

found a bug? not me manifesting 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). go off, file that report 💌

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👀 SEE ALSO 👀

domainseqs is fully documented via the tfm(1) system. iykyk 💅

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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. slay, honestly 🫶

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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. no cap 📜

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okay that's the whole thing bestie, every last flag accounted for, nothing skipped, we ate and left no crumbs 🍓✨

DOMAINATRIX 0.1.0+20100721 · 08/11/2010 — that's the version and date, mwah, love that for us 💜