Bio::A...ilities(3pm)

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

🌸 NAME 🌸

Bio::Align::Utilities — a whole lil grab-bag of utilities for converting and manipulating alignment objects. (the header line squishes it down to Bio::A...ilities(3pm) but bestie, you know the real name 💖)

✨ SYNOPSIS ✨

use Bio::Align::Utilities qw(:all);

# Even if the protein alignments are local make sure the start/end
# stored in the LocatableSeq objects are to the full length protein.
# The coding sequence that is passed in should still be the full
# length CDS as the nt alignment will be generated.
# %dnaseqs is a hash of CDS sequences (spliced)
my $dna_aln = aa_to_dna_aln($aa_aln,\%dnaseqs);

# The reverse, which is simpler. The input alignment has to be
# translate-able, with gap lengths and an overall length divisible by 3
my $aa_aln = dna_to_aa_aln($dna_al);

# Generate bootstraps
my $replicates = bootstrap_replicates($aln,$count);

💜 DESCRIPTION 💜

okay so this module is literally just a pile of utility methods for messing with sequence alignment objects — specifically Bio::Align::AlignI ones. that's the whole vibe 🫶

and the tea on aa_to_dna_aln: it's essentially doing the exact same job as the mrtrans program by Bill Pearson, which lives at ftp://ftp.virginia.edu/pub/fasta/other/mrtrans.shar. ours is a pure-Perl implementation, but the point of mentioning it is: if anything ever looks sus to you, you can go check your generated alignments against Bill's program. icon behavior honestly ✨

📬 FEEDBACK 📬

💌 Mailing Lists

user feedback is an integral part of the evolution of this and every other Bioperl module, fr fr. send your comments and suggestions preferably to the Bioperl mailing list — your participation is so appreciated, no cap 🥹

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

🫶 Support

please direct your usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

rather than sliding into the module maintainer's DMs directly, bestie. there are so many experienced and reponsive experts on there who will be able to look at your problem and quickly address it. and please include a thorough description of the problem, with code and data examples, if at all possible 🙏

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web:

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

👑 AUTHOR - Jason Stajich 👑

email: jason-at-bioperl-dot-org

📖 APPENDIX 📖

the rest of this documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk 💅)

🧬 aa_to_dna_aln

  • Title : aa_to_dna_aln
  • Usage : my $dnaaln = aa_to_dna_aln($aa_aln, \%seqs);
  • Function : will convert an AA alignment to DNA space given the corresponding DNA sequences.
heads up bestie: this method expects the DNA sequences to be in frame +1 (GFF frame 0), because it will start to project into coordinates starting at the first base of the DNA sequence. if this alignment represents a different frame for the cDNA, you're gonna need to edit the DNA sequences to remove the 1st or 2nd bases (and revcom if things should be). 😭
  • Returns : Bio::Align::AlignI object
  • Args : 2 arguments, the alignment and a hashref. the alignment is a Bio::Align::AlignI of amino acid sequences. the hash reference should have keys which are the display_ids for the aa sequences in the alignment, and the values are a Bio::PrimarySeqI object for the corresponding spliced cDNA sequence.

See also: Bio::Align::AlignI, Bio::SimpleAlign, Bio::PrimarySeq

🧬 dna_to_aa_aln

  • Title : dna_to_aa_aln
  • Usage : my $aa_aln = dna_to_aa_aln($dna_aln);
  • Function : convert a DNA alignment to an amino acid alignment, where the length of all alignment strings and the lengths of any gaps must be divisible by 3. that's the rule, periodt.
  • Returns : Bio::Align::AlignI object
  • Args : the DNA alignment, a Bio::Align::AlignI of DNA sequences

See also: Bio::Align::AlignI, Bio::SimpleAlign, Bio::PrimarySeq

🎲 bootstrap_replicates

  • Title : bootstrap_replicates
  • Usage : my $alns = &bootstrap_replicates($aln,100);
  • Function : generate a pseudo-replicate of the data by randomly sampling, with replacement, the columns from an alignment for the non-parametric bootstrap.
  • Returns : Arrayref of L<Bio::SimpleAlign> objects
  • Args : L<Bio::SimpleAlign> object
    • Number of replicates to generate

🎲 bootstrap_replicates_codons

  • Title : bootstrap_replicates_codons
  • Usage : my $alns = &bootstrap_replicates_codons($aln,100);
  • Function : generate a pseudo-replicate of the data by randomly sampling, with replacement, the columns from a codon alignment for the non-parametric bootstrap. the alignment is assumed to start on the first position of a codon. 🧬
  • Returns : Arrayref of L<Bio::SimpleAlign> objects
  • Args : L<Bio::SimpleAlign> object
    • Number of replicates to generate

🐱 cat

  • Title : cat
  • Usage : $aln123 = cat($aln1, $aln2, $aln3)
  • Function : concatenates alignment objects. sequences are identified by id. an error will be thrown if the sequence ids are not unique in the first alignment. if any ids are not present or not unique in any of the additional alignments, then those sequences are omitted from the concatenated alignment, and a warning is issued. an error will be thrown if any of the alignments are not flush, since concatenating such alignments is unlikely to make biological sense. 💀
  • Returns : a new Bio::SimpleAlign object
  • Args : a list of Bio::SimpleAlign objects

🌟 most_common_sequences

  • Title : most_common_sequences
  • Usage : @common = most_common_sequences ($align, $case_sensitivity)
  • Function : returns an array of the sequences that appear most often in the alignment (although this probably makes more sense when there is only a single most common sequence). sequences are compared after removing any "-" (gap characters), and ambiguous units (e.g., R for purines) are only compared to themselves. the returned sequence is also missing the "-" since they don't actually make part of the sequence. ✨
  • Returns : array of text strings.
  • Arguments : optional argument defining whether the comparison between sequences to find the most common should be case sensitive. defaults to false, i.e, not case sensitive.

and that's the whole page, bestie!! this was rendered by perl v5.32.1 back on 2021-08-15, and the man page header was doing its lil Bio::A...ilities(3pm) abbreviation thing the whole time. go forth and align your sequences, you absolute icon 🎀💖✨

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