SSEMATCH(1e)

👑 SSEMATCH — the manual page, bestie edition 💅

okay so like. hi. you're reading the ssematch(1e) page from the EMBOSS Manual for Debian and honestly? slay. let's get into it.

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✨ NAME ✨

ssematch — search a DCF file for secondary structure matches. that's it, that's the whole job. 🎀

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🦋 SYNOPSIS 🦋

ssematch -ssinfile infile -dcfinfile infile [-datafile matrixf]
         -maxhits integer [-rgapopen float] [-rgapextend float]
         [-egapopen float] [-egapextend float] -outssfile outfile
         -outsefile outfile -logfile outfile

ssematch -help

like, you could just run it with -help if you're feeling lazy. no judgement. 💖

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🌸 DESCRIPTION 🌸

ssematch is a command line program from EMBOSS (aka “the European Molecular Biology Open Software Suite”). it lives in the "Utils:Database creation" command group(s), so that's its little clique. 🫶

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💅 OPTIONS 💅

🍓 Input section

• -ssinfile infile — this one names the file of secondary structure (input). literally what you're feeding it.
• -dcfinfile infile — names the DCF file (domain classification file) (input). quick vocab check: a 'domain classification file' holds classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). those files get generated by using SCOPPARSE and CATHPARSE, and you can add domain sequence information to the file by using DOMAINSEQS. iykyk. ✨
• -datafile matrixf — this names the secondary structure substitution matrix. default value: SSSUB. she's got a default, she's low maintenance.

🧚 Required section

• -maxhits integer — how many top-scoring matches to report. default value: 5. only the besties make the cut. 👑

🌈 Additional section

• -rgapopen float — the gap insertion penalty for reside-based alignment. the gap insertion 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: 10.
• -rgapextend float — the gap extension penalty for residue-based alignment. 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. default value: 0.5.
• -egapopen float — the gap insertion penalty for element-based alignment. the gap insertion 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: 10.
• -egapextend float — the gap extension penalty for secondary structure element-based alignment. 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. default value: 0.5.

not me writing "reside-based" in the first one and "residue-based" in the second — that's just what the page says, bestie, i keep the lore exact. 😭

🎀 Output section

• -outssfile outfile — names the file containing top-scoring domains for residue-based alignment (output). heads up: a 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like).
• -outsefile outfile — names the file containing top-scoring domains for secondary structure element-based alignment (output). and again, a 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like).
• -logfile outfile — names the ssematch log file (output). default value: ssematch.log. she journals. 💜

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💀 BUGS 💀

found a bug? report it to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or slide directly into the EMBOSS developers' DMs (http://sourceforge.net/tracker/?group_id=93650&atid=605031). they want to know. fr fr.

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🔥 SEE ALSO 🔥

ssematch is fully documented via the tfm(1) system. go read that too, 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. iconic behaviour 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.

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okay and the lil' sign-off at the bottom of the page: this whole thing comes from DOMAINATRIX 0.1.0+20100721, dated 08/11/2010. yes, she's vintage. vintage is a vibe. 💅✨ take care of her, mwah. 🫶