Bio::T...::Exon(3pm)

💖 NAME 💖

Bio::Tools::Prediction::Exon — a predicted exon feature, bestie. It's literally the glow-up version of an exon that a program guessed at. 🔥

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✨ SYNOPSIS ✨

# See documentation of methods.

Yeah that's it, that's the synopsis. The methods are down below in the APPENDIX, keep scrolling. 🫶

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🌸 DESCRIPTION 🌸

Okay so picture this: a feature that represents a predicted exon. This class actually inherits off Bio::SeqFeature::Gene::Exon, so it gets all of that functionality for free — and yes, that means it also implements Bio::SeqFeatureI too, no cap. 💅

On top of all that inherited goodness, it adds a few extra methods that exist specifically to support predicted features — stuff like various scores and a significance. Those were inspired by GenScan results, but ngl, at least a subset of them should be generally useable for exon prediction results in general. 🌈

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🎀 FEEDBACK 🎀

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. So send your comments and suggestions preferably to one of the Bioperl mailing lists — your participation is much appreciated, fr fr. 🥹

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

🫶 Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

…rather than to the module maintainer directly. The reason is lowkey iconic: many experienced and reponsive experts will be able look at the problem and quickly address it. 👑 Please include a thorough description of the problem with code and data examples if at all possible. (yes, code and data examples, they're not being extra, they genuinely help)

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

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

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🌟 AUTHOR - Hilmar Lapp 🌟

Email hlapp-at-gmx.net

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — iykyk. 💀

🧬 predicted_cds

• Title: predicted_cds
• Usage:

$predicted_cds_dna = $exon->predicted_cds();
$exon->predicted_cds($predicted_cds_dna);

• Function: Get/Set the CDS (coding sequence) as predicted by a program.

Heads up bestie: this method is independent of an attached_seq. There is no guarantee whatsoever that the returned CDS has anything to do (e.g., matches) with the sequence covered by the exons as annotated through this object. 😭

• Example:
• Returns: A Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program.
• Args: On set, a Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program.

🧬 predicted_protein

• Title: predicted_protein
• Usage:

$predicted_protein_seq = $exon->predicted_protein();
$exon->predicted_protein($predicted_protein_seq);

• Function: Get/Set the protein translation as predicted by a program.

Okay so again: this method is independent of an attached_seq. There is no guarantee whatsoever that the returned translation has anything to do with the sequence covered by the exons as annotated through this object, or the sequence returned by predicted_cds(), although it should usually be just the standard translation. 🙈

• Example:
• Returns: A Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program.
• Args: On set, a Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program.

⭐ significance

• Title: significance
• Usage:

$evalue = $obj->significance();
$obj->significance($evalue);

• Function:
• Returns:
• Args:

🚦 start_signal_score

• Title: start_signal_score
• Usage:

$sc = $obj->start_signal_score();
$obj->start_signal_score($evalue);

• Function: Get/Set a score for the exon start signal (acceptor splice site or initiation signal).
• Returns:
• Args:

🏁 end_signal_score

• Title: end_signal_score
• Usage:

$sc = $obj->end_signal_score();
$obj->end_signal_score($evalue);

• Function: Get/Set a score for the exon end signal (donor splice site or termination signal).
• Returns:
• Args:

💫 coding_signal_score

• Title: coding_signal_score
• Usage:

$sc = $obj->coding_signal_score();
$obj->coding_signal_score($evalue);

• Function: Get/Set a score for the exon coding signal (e.g., coding potential).
• Returns:
• Args:

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That's the whole page, babe — perl v5.32.1, dated 2021-08-15, Bio::Tools::Prediction::Exon(3pm), brought to you by the good people of User Contributed Perl Documentation. Go predict some exons, you absolute icon. 💅✨