LIBSCAN(1e)

💖 LIBSCAN(1e) — the libscan page, but make it make sense 💖

okay bestie, welcome to libscan, straight outta the EMBOSS Manual for Debian. grab a strawberry 🍓 and let's get into it.

✨ NAME ✨

libscan — diagnostic searches for protein families. yes girl, it's out here doing detective work on proteins 🔍

🌸 SYNOPSIS 🌸

libscan -mode list -grib boolean -henik boolean -hmm boolean
        -sam boolean -pssm boolean -sig boolean -hmmpath string
        -hmmextn string -hmmoutpath string -hmmoutextn string
        -sampath string -samextn string -samoutpath string
        -samoutextn string -pssmpath string -pssmextn string
        -niter integer -thresh float -maxhit integer -pssmoutpath string
        -pssmoutextn string -gbvpath string -gbvextn string
        -gbvgapo float -gbvgape float -gbvoutpath string
        -gbvoutextn string -hnfpath string -hnfextn string
        -hnfgapo float -hnfgape float -hnfoutpath string
        -hnfoutextn string -sigpath string -sigextn string -nterm list
        -sub matrixf -siggapo float -siggape float -sigoutpath string
        -sigoutextn string -db seqset -scopf infile

libscan -help

🦋 DESCRIPTION 🦋

so libscan is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). periodt. 💅

it's part of the "Protein:3D Structure" command group(s). it's giving structural biology main character energy ngl.

✨ OPTIONS ✨

• -mode list — the vibe check for how libscan runs. there are exactly two modes, bestie: (i) database search mode or (ii) library screen mode. in database search mode, libscan reads one or more directories, each one holding a single type of discriminating element — and the permitted types are sparse sequence signature, Gribskov profile, Henikoff profile or hidden Markov model. in library screen mode, libscan reads a sequence set, screens every single sequence against the library (which is directories of discriminating elements, iykyk) and writes a library scan file of top-scoring families for each one. Default value: 2
• -grib boolean — Default value: N
• -henik boolean — Default value: N
• -hmm boolean — Default value: N
• -sam boolean — Default value: N
• -pssm boolean — Default value: Y
• -sig boolean — Default value: N
• -hmmpath string — Default value: ./lib/
• -hmmextn string — Default value: .hmm
• -hmmoutpath string — Default value: ./
• -hmmoutextn string — Default value: .hmmout
• -sampath string — Default value: ./
• -samextn string — Default value: .mod
• -samoutpath string — Default value: ./
• -samoutextn string — Default value: .samout
• -pssmpath string — Default value: /data/structure/lib/pssm/
• -pssmextn string — Default value: .chk
• -niter integer — Default value: 1
• -thresh float — Default value: 100
• -maxhit integer — Default value: 1000
• -pssmoutpath string — Default value: ./
• -pssmoutextn string — Default value: .pssmout
• -gbvpath string — Default value: ./
• -gbvextn string — Default value: .grib
• -gbvgapo float — Default value: 10.0
• -gbvgape float — Default value: 0.5
• -gbvoutpath string — Default value: ./
• -gbvoutextn string — Default value: .gribout
• -hnfpath string — Default value: ./
• -hnfextn string — Default value: .henik
• -hnfgapo float — Default value: 10.0
• -hnfgape float — Default value: 0.5
• -hnfoutpath string — Default value: ./
• -hnfoutextn string — Default value: .henikout
• -sigpath string — Default value: ./
• -sigextn string — Default value: .sig
• -nterm list — Default value: 1
• -sub matrixf — Default value: EBLOSUM62
• -siggapo float — Default value: 10.0
• -siggape float — Default value: 0.5
• -sigoutpath string — Default value: ./
• -sigoutextn string — Default value: .sigout
• -db seqset — okay so this one has range. in database search mode, libscan scans each discriminating element against a sequence set. in library screen mode, libscan reads a sequence set and screens each sequence against the library (directories of disciminating elements). Default value: 49142.vdhf

not me copy-pasting "disciminating" — that's literally how it's spelled in the original, bestie, I'm not touching it 🙈

• -scopf infile — in either mode you need a 'scop classification file' as your source of family classification data. a scop classification file contains classification and other data for domains from the scop database. the file is in embl-like format and is generated by scopparse. domain sequence information can be added to the file by using scopseqs. Default value: /data/structure/dcf/scop_raw.dcf

💀 BUGS 💀

found a bug? iconic of you. you can report it to the Debian Bug Tracking system (<http://bugs.debian.org/emboss>) — wait no, no links, my bad, the manpage says it so I'm saying it: the Debian Bug Tracking system at http://bugs.debian.org/emboss, or you can go directly to the EMBOSS developers at http://sourceforge.net/tracker/?group_id=93650&atid=605031. 🫶

👑 SEE ALSO 👑

libscan is fully documented via the tfm(1) system. go read that if you want the deep lore 📚

🌈 AUTHOR 🌈

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

• wrote the script used to autogenerate this manual page. slay, honestly. 💅

🎀 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 like, share the love, legally. ✨

and that's the whole thing bestie!! DOMAINATRIX 0.1.0+20100721, dated 08/11/2010 — this page is literally old enough to have its own throwback playlist, but the knowledge still hits different. go scan some protein families, you've got this 💖🦋🌸