Bio::S...:Intron(3pm)

💖 Bio::S...:Intron 💖

okay bestie, welcome to the Bio::S...:Intron(3pm) page, straight out of the User Contributed Perl Documentation section 🎀 this is the whole vibe, let's get into it

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✨ NAME ✨

Bio::SeqFeature::Gene::Intron — it's an intron feature, periodt 🧬

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🌸 SYNOPSIS 🌸

Give standard usage here

(yes bestie, that's literally what the page says, we're not making stuff up, that's the whole synopsis 😭)

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🦋 DESCRIPTION 🦋

Describe the object here

(again, fr fr, that's what it says, no notes 💀)

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💌 FEEDBACK 💌

📬 Mailing Lists

user feedback is like, the whole backbone of how this module and every other Bioperl module evolves, no cap 🫶 so please send your comments and suggestions, preferably to the Bioperl mailing list. your participation is so appreciated, genuinely.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🫂 Support

okay so if you've got usage questions or support issues, please direct them to the mailing list:

bioperl-l@bioperl.org

and not straight to the module maintainer, bestie 🙈 because there are so many experienced and responsive experts on that list who can look at your problem and address it quickly. and if you can, include a thorough description of the problem with code and data examples — that's the good stuff, it helps so much.

🐛 Reporting Bugs

spotted a bug? report it to the Bioperl bug tracking system so they can keep track of the bugs and their resolutions. bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

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👑 AUTHOR — David Block 👑

Email: dblock@gene.pbi.nrc.ca

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods, and internal methods are usually preceded with a _ 💅

🧵 upstream_Exon

Title   : upstream_Exon
Usage   : $intron->upstream_Exon()
Function: exon upstream of the intron
Returns : Bio::EnsEMBL::Exon
Args    :

🧵 downstream_Exon

Title   : downstream_Exon
Usage   : $intron->downstream_Exon()
Function: exon downstream of the intron
Returns : Bio::EnsEMBL::Exon
Args    :

🌈 phase

Title   : phase
Usage   : $intron->phase()
Function: returns the phase of the intron(where it interrupts the codon)
Returns : int(0,1,2)
Args    :

🎀 acceptor_splice_site

Title   : acceptor_splice_site
Usage   : $intron->acceptor_splice_site(21,3)
Function: returns the sequence corresponding to the
          consensus acceptor splice site. If start and
          end are provided, it will number of base pairs
          left and right of the canonical AG. Here 21 means
          21 bp into intron and 3 means 3 bp into the exon.
          --Intron--21----|AG|-3-----Exon
          Defaults to 21,3

Returns : Bio::Seq
Args    : start and end

🎀 donor_splice_site

Title   : donor_splice_site
Usage   : $intron->donor_splice_site(3,6)
Function: returns the sequence corresponding to the
          consensus donor splice site. If start and
          end are provided, it will number of base pairs
          left and right of the canonical GT. Here 3 means
          3 bp into exon and 6 means 6 bp into the intron.
          --Exon-3--|GT|-6----Intron-
          Defaults to 3,6

Returns : Bio::Seq
Args    : start and end

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and that's the whole page, bestie, we ate and left no crumbs 💅✨ this was perl v5.32.1, dated 2021-08-15 — sending you off with all the love, mwah 🫶💖