SEQSORT(1e)

💖 SEQSORT(1e) 💖

okay bestie, welcome to the EMBOSS Manual for Debian — this is the page for seqsort, and yes it's a whole vibe, let's get into it 🦋

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✨ NAME ✨

seqsort — Remove ambiguous classified sequences from DHF files. that's it, that's the job, and it does it flawlessly 💅

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🎀 SYNOPSIS 🎀

seqsort -dhfindir directory -overlap integer -dofamilies toggle
        -doambiguities toggle -dhfoutdir outdir -hitsfile outfile
        -ambigfile outfile

seqsort -help

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🌸 DESCRIPTION 🌸

So seqsort is a command line program from EMBOSS, aka "the European Molecular Biology Open Software Suite" — iconic name, no notes. It lives in the "Protein:3D Structure" command group(s), so that's its little clique 🫶

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✨ OPTIONS ✨

💜 Input section

• -dhfindir directory — tells it where the DHF files live (domain hits files), and yeah this is the input. A 'domain hits file' is full of database hits (sequences) that come with domain classification info, all in DHF format (FASTA or EMBL-like, either one slays). Those hits are relatives to a SCOP or CATH family and they got found by searching a sequence database. And the files with hits retrieved by PSIBLAST? Those get generated by using SEQSEARCH 👑 Default value: ./

💖 Required section

• -overlap integer — how many overlapping residues you need before two hits get merged. Every family also gets processed so that overlapping hits (hits with identical accesssion number that overlap by at least a user-defined number of residues — yes, spelling is exactly like that in the original, we don't touch it) get swapped out for a hit produced from merging those two overlapping hits. Default value: 10
• -dofamilies toggle — do you want a domain families file written? Set this and boom, a domain families file gets written. Default value: N
• -doambiguities toggle — do you want a domain ambiguities file</ma> written? Set this and boom, a domain ambiguities file gets written. Default value: N

🦋 Output section

• -dhfoutdir outdir — where the DHF files go on the way out (domain hits files). 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: ./
• -hitsfile outfile — the name of the domain families file (output). A 'domain families file' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e.g. by using SEQSEARCH (psiblast). The file contains the collated search results for the indvidual families — only the hits of unambiguous family assignment make the cut. Hits with ambiguous family assignment get assigned as relatives to a SCOP or CATH superfamily or fold instead, and they get collated into a 'domain ambiguities file'. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file). Default value: fam.dhf
• -ambigfile outfile — the name of the domain ambiguities file (output). A 'domain families file' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e.g. by using SEQSEARCH (psiblast). The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file). Default value: oth.dhf

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💀 BUGS 💀

Found a bug? 😭 Do NOT suffer in silence, report it to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or go straight to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). They wanna hear from you fr fr 🫶

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🔥 SEE ALSO 🔥

seqsort 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. (not me writing this page tho, that's all me 💅)

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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. periodt.

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and that's the whole page bestie!! 🎀 this was DOMSEARCH 0.1.0++20100721, dated 08/11/2010, and it's the SEQSORT(1e) page — mwah, go sort some sequences, you got this 💖✨🦋