SEQALIGN(1e)

📦 version 0.1.660, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 SEQALIGN(1e) — like, the whole vibe 💖

EMBOSS Manual for Debian, bestie. Yes, we're doing this. Grab a snack 🍓

✨ NAME ✨

seqalign — extends alignments (DAF file) with sequences (DHF file). That's the whole job. She's a connector. A matchmaker. 🫶

🌸 SYNOPSIS 🌸

Okay so here's how you actually call her:

seqalign -mode list -dhfinpath dirlist -dafinpath dirlist
         -dhfindir directory -amode list [-forcetype boolean]
         -dafoutdir outdir -logfile outfile

and also, for when you just need emotional support:

seqalign -help

🦋 DESCRIPTION 🦋

seqalign is a command line program from EMBOSS, aka “the European Molecular Biology Open Software Suite”. It lives in the "Protein:3D Structure" command group(s), which is honestly such a specific little neighborhood and I respect it 💅

👑 OPTIONS 👑

🌈 Input section

  • -mode list — bestie, this picks the mode of SEQALIGN operation. SEQALIGN takes as input a directory of either i. single sequences, or ii. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file)). The user has to specify which. Default value: 1
  • -dhfinpath dirlist — where the sequences live, e.g. DHF files (domain hits files) (input). SEQALIGN takes as input a database of either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Default value: ./
  • -dafinpath dirlist — where the sequences live, e.g. DAF files (domain alignment files) (input). SEQALIGN takes as input a database of either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Default value: ./
  • -dhfindir directory — where the DHF files (domain hits files) live (input). 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: ./

💜 Required section

  • -amode list — which alignment algorithm are we using, queen? This option specifies it. Default value: 1

⭐ Additional section

  • -forcetype boolean — do we force minimal domain classification data to be written to the output file in cases where singlet sequences were given as input file and no classification data was available? That's literally the whole question this option asks. Default value: N

🎀 Output section

  • -dafoutdir outdir — where the DAF files (domain alignment files) go (output). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Default value: ./
  • -logfile outfile — the name of the log file for the build. The log file contains messages about any errors arising while SEQALIGN ran. Default value: seqalign.log

💀 BUGS 💀

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). Not me manifesting bugs, just being thorough 🙈

🔥 SEE ALSO 🔥

seqalign is fully documented via the tfm(1) system. iykyk ✨

🧚 AUTHOR 🧚

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

  • Wrote the script used to autogenerate this manual page. Iconic of them honestly 👑

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.

Okay that's the whole page!! Signing off from DOMALIGN 0.1.0+20100721, dated 08/11/2010 — she's an elder but she still ate 💅✨ no cap, go extend some alignments bestie 🌈🦋💖

📦 where this page comes from