DOMAINALIGN(1e)

💖 DOMAINALIGN 💖

okay bestie, welcome to the manual page for domainalign, straight outta the EMBOSS Manual for Debian ✨ this is section 1e of the manual, and it's literally the glow-up guide for generating alignments (a DAF file, no less) for nodes in a DCF file. let's get into it 🫶

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✨ NAME ✨

domainalign — Generate alignments (DAF file) for nodes in a DCF file.

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🌸 SYNOPSIS 🌸

domainalign -dcfinfile infile -pdbdir directory -node list -mode list
            -keepsinglets toggle -dafoutdir outdir
            -singletsoutdir outdir -superoutdir outdir -logfile outfile

domainalign -help

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🦋 DESCRIPTION 🦋

domainalign is a command line program from EMBOSS — that's “the European Molecular Biology Open Software Suite,” bestie, the whole suite, iconic behavior 💅

it's part of the "Protein:3D Structure" command group(s), so you already know it's doing the most with protein structures 🔥

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🎀 OPTIONS 🎀

💜 Input section 💜

• -dcfinfile infile — this one's the name of your DCF file (that's the domain classification file), and it's your input 💖 a 'domain classification file' holds classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). where do these files come from? you generate them by using SCOPPARSE and CATHPARSE, periodt. and if you want domain sequence info in there too, you add it to the file by using DOMAINSEQS ✨
• -pdbdir directory — specifies the location of domain PDB files (input). a 'domain PDB file' contains coordinate data for a single domain from SCOP or CATH, in PDB format. these files get generated by using DOMAINER. default value: ./ 🌸

👑 Required section 👑

• -node list — specifies the node for redundancy removal. you can remove redundancy at any node you want in the SCOP or CATH hierarchies, like, pick your spot bestie. for example, by selecting 'Class' entries belonging to the same Class will be non-redundant. default value: 1
• -mode list — specifies the alignment algorithm to use. default value: 1 🌈
• -keepsinglets toggle — specifies whether to write sequences of singlet families to file. if you specify this option, the sequence for each singlet family are written to file (output). default value: Y 🎀

💖 Output section 💖

• -dafoutdir outdir — specifies the location of DAF files (domain alignment files) (output). a 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. these files are in clustal format and are annotated with domain family classification information. and get this — the files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. you can extend such alignments with sequence relatives (of unknown structure) by using SEQALIGN ✨ default value: ./
• -singletsoutdir outdir — specifies the location of DHF files (domain hits files) for singlet sequences (output). the singlets get written out as a 'domain hits file' — which contains database hits (sequences) with domain classification information, in FASTA format. default value: ./ 🦋
• -superoutdir outdir — specifies the location of structural superimposition files (output). a file in PDB format of the structural superimposition is generated for each family if the STAMP algorithm is used. default value: ./ 🔥
• -logfile outfile — specifies the name of the log file (output). the log file contains messages about any errors arising while domainalign ran. default value: domainalign.log 💅

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💀 BUGS 💀

found a bug? no worries, it happens to the best of us. report it to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or slide directly into the EMBOSS developers' DMs at (http://sourceforge.net/tracker/?group_id=93650&atid=605031) 🙈

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🧚 SEE ALSO 🧚

domainalign is fully documented via the tfm(1) system. go check it out, 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. shoutout to the script bestie, it ate 🫶

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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. (so yes, go off, but respectfully 💜)

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and that's the whole vibe check, bestie 🎀 this was DOMALIGN 0.1.0+20100721, dated 08/11/2010, living its life as DOMAINALIGN(1e) in the manual. slay, stay aligned, and go generate those DAF files ✨💖👑