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

okay so bestie 💖 you just opened the User Contributed Perl Documentation page for Bio::Tools::OddCodes, and honestly? it's giving niche-but-iconic. let's get into it 🧬✨

🌸 NAME 🌸

Bio::Tools::OddCodes — an object holding alternative alphabet coding for one protein sequence 👑

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✨ SYNOPSIS ✨

bestie, the vibe is: you take a sequence object (from an inputstream, or wherever), and you make an object whose whole job is rewriting that sequence in a different alphabet. these are abbreviated amino acid sequence alphabets — designed to make the stats side of protein analysis less of a nightmare, by cutting down the combinatorial explosion of the 20-letter alphabet. these abbreviated alphabets range in size from 2 to 8 🎀

# Take a sequence object from eg, an inputstream, and creates a
# object for the purposes of rewriting that sequence in another
# alphabet.  These are abbreviated amino acid sequence alphabets,
# designed to simplify the statistical aspects of analysing protein
# sequences, by reducing the combinatorial explosion of the
# 20-letter alphabet.  These abbreviated alphabets range in size
# from 2 to 8.

# Creating the OddCodes object, eg:

      my $inputstream = Bio::SeqIO->new( '-file' => "seqfile",
                                         '-format' => 'Fasta');
      my $seqobj = $inputstream->next_seq();
      my $oddcode_obj = Bio::Tools::Oddcodes->new(-seq => $seqobj);

# or:

      my $seqobj = Bio::PrimarySeq->new
            (-seq=>'[cut and paste a sequence here]',
             -alphabet => 'protein',
             -id => 'test');
      my $oddcode_obj  =  Bio::Tools::OddCodes->new(-seq => $seqobj);

# do the alternative coding, returning the answer as a reference to
# a string

      my $output = $oddcode_obj->structural();
      my $output = $oddcode_obj->chemical();
      my $output = $oddcode_obj->functional();
      my $output = $oddcode_obj->charge();
      my $output = $oddcode_obj->hydrophobic();
      my $output = $oddcode_obj->Dayhoff();
      my $output = $oddcode_obj->Sneath();
      my $output = $oddcode_obj->Stanfel();

# display sequence in new form, eg:

      my $new_coding = $$output;
      print "\n$new_coding";

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💜 DESCRIPTION 💜

Bio::Tools::Oddcodes is a welterweight object for rewriting a protein sequence in an alternative alphabet. eight of those alphabets are provided, ranging all the way from the 2-letter hydrophobic alphabet up to the 8-letter chemical alphabet 🌈 these are genuinely useful for the statistical analysis of protein sequences, because they can partially dodge the combinatorial explosion that the full 20-letter alphabet gives you (like, we're talking 400 dimers, 8000 trimers, etc.) 😭 the math was mathing too hard.

if the input sequence is not a protein, the object will print out a warning. if you know what you're doing, you can silence that warning by setting verbose() to a negative value 🤫

and yeah — see the SYNOPSIS above for the object creation code, it's all there 🫶

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📚 REFERENCES 📚

• Stanfel LE (1996) A new approach to clustering the amino acids. J. theor. Biol. 183, 195-205.
• Karlin S, Ost F and Blaisdell BE (1989) Patterns in DNA and amino acid sequences and their statistical significance. Chapter 6 of: Mathematical Methods for DNA Sequences. Waterman MS (ed.) CRC Press, Boca Raton , FL.

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💌 FEEDBACK 💌

📬 Mailing Lists 📬

user feedback is, like, an integral part of the evolution of this and other Bioperl modules — genuinely. send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated 💖

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. so many experienced and responsive experts will be able to look at the problem and quickly address it 👑 and if it's at all possible, please include a thorough description of the problem with code and data examples. the more detail the better, no cap.

🐛 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

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✍️ AUTHOR ✍️

Derek Gatherer 💅

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🧚 APPENDIX 🧚

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

structural 🦋

• Title: structural
• Usage: $output = $oddcode_obj->structural();
• Function: turns amino acid sequence into 3-letter structural alphabet: A (ambivalent), E (external), I (internal)
• Example: a sequence ACDEFGH will become AAEEIAE
• Returns: Reference to the new sequence string
• Args: none

functional 🍓

• Title: functional
• Usage: $output = $oddcode_obj->functional();
• Function: turns amino acid sequence into 4-letter functional alphabet: A (acidic), C (basic), H (hydrophobic), P (polar)
• Example: a sequence ACDEFGH will become HPAAHHC
• Returns: Reference to the new sequence string
• Args: none

hydrophobic 💧

• Title: hydrophobic
• Usage: $output = $oddcode_obj->hydrophobic();
• Function: turns amino acid sequence into 2-letter hydrophobicity alphabet: O (hydrophobic), I (hydrophilic)
• Example: a sequence ACDEFGH will become OIIIOII
• Returns: Reference to the new sequence string
• Args: none

Dayhoff ⭐

• Title: Dayhoff
• Usage: $output = $oddcode_obj->Dayhoff();
• Function: turns amino acid sequence into 6-letter Dayhoff alphabet
• Example: a sequence ACDEFGH will become CADDGCE
  • A (=C), C (=AGPST), D (=DENQ),
  • E (=HKR), F (=ILMV), G (=FWY)
• Returns: Reference to the new sequence string
• Args: none

Sneath 🌸

• Title: Sneath
• Usage: $output = $oddcode_obj->Sneath();
• Function: turns amino acid sequence into 7-letter Sneath alphabet
• Example: a sequence ACDEFGH will become CEFFHCF
  • A (=ILV), C (=AGP), D (=MNQ), E (=CST),
  • F (=DE), G (=KR), H (=FHWY)
• Returns: Reference to the new sequence string
• Args: none

Stanfel 👑

• Title: Stanfel
• Usage: $output = $oddcode_obj->Stanfel();
• Function: turns amino acid sequence into 4-letter Stanfel alphabet
• Example: a sequence ACDEFGH will become AACCDAE
  • A (=ACGILMPSTV), C (=DENQ), D (=FWY), E (=HKR)
• Returns: Reference to the new sequence string
• Args: none

chemical 🧪

• Title: chemical
• Usage: $output = $oddcode_obj->chemical();
• Function: turns amino acid sequence into 8-letter chemical alphabet: A (acidic), L (aliphatic), M (amide), R (aromatic), C (basic), H (hydroxyl), I (imino), S (sulphur)
• Example: a sequence ACDEFGH will become LSAARAC
• Returns: Reference to the new sequence string
• Args: none

charge ⚡

• Title: charge
• Usage: $output = $oddcode_obj->charge();
• Function: turns amino acid sequence into 3-letter charge alphabet
• Example: a sequence ACDEFGH will become NNAANNC
  • A (negative; NOT anode), C (positive; NOT cathode), N (neutral)
• Returns: Reference to the new sequence string
• Args: none

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⚠️ quick lil reminder bestie: those NOT anode / NOT cathode notes on charge are doing real work — don't go reading A and C as electrodes, okay? 🙈

and that's the whole page, we ate and left no crumbs 💅 this was perl v5.32.1, dated 2021-08-15 — mwah, bye bestie 🎀✨🦋