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

🌈 NAME 🌈

Bio::Tools::Sigcleave — the Bioperl object for sigcleave analysis 💖

(yes the manpage header is filed under Bio::T...gcleave(3pm) — she's just being mysterious, it's the same girlie 🫶)

---

✨ SYNOPSIS ✨

🎀 Object Creation

use Bio::Tools::Sigcleave ();

# to keep the module backwar compatible, you can pass it a sequence string, but
# there recommended say is to pass it a Seq object

# this works
$seq = "MVLLLILSVLLLKEDVRGSAQSSERRVVAHMPGDIIIGALFSVHHQPTVDKVHERKCGAVREQYGI";
$sig = Bio::Tools::Sigcleave->new(-seq  => $seq,
                                  -type => 'protein',
                                  -threshold=>'3.5',
                                  );
# but you do:
$seqobj = Bio::PrimarySeq->new(-seq => $seq);

$sig = Bio::Tools::Sigcleave->new(-seq  => $seqobj,
                                  -threshold=>'3.5',
                                  );

okay so real talk bestie — passing a plain sequence string only works because the module is keeping it backwar compatible (their spelling, not mine, I would never 😭). The recommended say is to pass it a Seq object instead. Both doors are open, one is just the ✨main character✨ door.

# now you can detect procaryotic signal sequences as well as eucaryotic
$sig->matrix('eucaryotic'); # or 'procaryotic'

💅 Object Methods & Accessors

# you can use this method to fine tune the threshod before printing out the results
$sig->result_count:

%raw_results      = $sig->signals;
$formatted_output = $sig->pretty_print;

---

🧚 DESCRIPTION 🧚

Sigcleave was a program distributed as part of the free EGCG add-on to earlier versions of the GCG Sequence Analysis package. A new implementation of the algorithm is now part of EMBOSS package. slay, algorithm got a glow-up 💅

Straight from the EGCG documentation:

SigCleave uses the von Heijne method to locate signal sequences, and to identify the cleavage site. The method is 95% accurate in resolving signal sequences from non-signal sequences with a cutoff score of 3.5, and 75-80% accurate in identifying the cleavage site. The program reports all hits above a minimum value.

The EGCG Sigcleave program was written by Peter Rice (E-mail: pmr@sanger.ac.uk Post: Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs, CB10 1SA, UK). giving original author energy fr fr 👑

Since EGCG is no longer distributed for the latest versions of GCG, this code was developed to emulate the output of the original program as much as possible for those who lost access to sigcleave when upgrading to newer versions of GCG. a resurrection arc, we love to see it ✨

There are 2 accessor methods for this object. signals will return a perl associative array containing the sigcleave scores keyed by amino acid position. pretty_print returns a formatted string similar to the output of the original sigcleave utility.

In both cases, the threshold setting controls the score reporting level. If no value for threshold is passed in by the user, the code defaults to a reporting value of 3.5.

In this implementation the accessor will never return any score/position pair which does not meet the threshold limit. This is the slightly different from the behaviour of the 8.1 EGCG sigcleave program which will report the highest of the under-threshold results if nothing else is found. so if you're out here expecting under-threshold crumbs, no ma'am, this version simply will not 🙈

Example of pretty_print output:

        SIGCLEAVE of sigtest from: 1 to 146

        Report scores over 3.5
        Maximum score 4.9 at residue 131

         Sequence:  FVILAAMSIQGSA-NLQTQWKSTASLALET
                    | (signal)    | (mature peptide)
                118            131

         Other entries above 3.5

        Maximum score 3.7 at residue 112

         Sequence:  CSRQLFGWLFCKV-HPGAIVFVILAAMSIQGSANLQTQWKSTASLALET
                   | (signal)    | (mature peptide)
                99            112

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🌸 FEEDBACK 🌸

When updating and maintaining a module, it helps to know that people are actually using it. Let us know if you find a bug, think this code is useful or have any improvements/features to suggest. the devs literally just want a little "hey I used this" text, give them the serotonin 🫶

🦋 Support

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

bioperl-l@bioperl.org

rather than to the module maintainer directly. 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. code and data examples = the receipts, bring them 💅

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track 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 👑

Chris Dagdigian, dag-at-sonsorol.org & others

💖 CONTRIBUTORS 💖

Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

⭐ VERSION ⭐

Bio::Tools::Sigcleave, $Id$

🎀 COPYRIGHT 🎀

Copyright (c) 1999 Chris Dagdigian & others. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

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🔥 REFERENCES / SEE ALSO 🔥

• von Heijne G. (1986) "A new method for predicting signal sequences cleavage sites." Nucleic Acids Res. 14, 4683-4690.
• von Heijne G. (1987) in "Sequence Analysis in Molecular Biology: Treasure Trove or Trivial Pursuit" (Acad. Press, (1987), 113-117).

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🧁 APPENDIX 🧁

The following documentation describes the various functions contained in this module. Some functions are for internal use and are not meant to be called by the user; they are preceded by an underscore (_). iykyk — if it starts with an underscore, hands off bestie 🙅

🌟 threshold

• Title: threshold
• Usage: $value = $self->threshold
• Purpose: Read/write method sigcleave score reporting threshold.
• Returns: float.
• Argument: new value, float
• Throws: on non-number argument
• Comments: defaults to 3.5
• See Also: n/a

🌟 matrix

• Title: matrix
• Usage: $value = $self->matrix('procaryotic')
• Purpose: Read/write method sigcleave matrix.
• Returns: float.
• Argument: new value: 'eucaryotic' or 'procaryotic'
• Throws: on non-number argument
• Comments: defaults to 3.5
• See Also: n/a

🌟 seq

• Title: seq
• Usage: $value = $self->seq($seq_object)
• Purpose: set the Seq object to be used
• Returns: Seq object
• Argument: protein sequence or Seq object
• See Also: n/a

🌟 _Analyze

• Title: _Analyze
• Usage: N/A This is an internal method. Not meant to be called from outside the package
• Purpose: calculates sigcleave score and amino acid position for the given protein sequence. The score reporting threshold can be adjusted by passing in the "threshold" parameter during object construction. If no threshold is passed in, the code defaults to reporting any scores equal to or above 3.5
• Returns: nothing. results are added to the object
• Argument: none.
• Throws: nothing.
• Comments: nothing.
• See Also: n/a

🌟 signals

• Title: signals
• Usage: %sigcleave_results = $sig->signals;
• Purpose: Accessor method for sigcleave results
• Returns: Associative array. The key value represents the amino acid position and the value represents the score. Only scores that are greater than or equal to the THRESHOLD value are reported.
• Argument: none.
• Throws: none.
• Comments: none.
• See Also: THRESHOLD

🌟 result_count

• Title: result_count
• Usage: $count = $sig->result_count;
• Purpose: Accessor method for sigcleave results
• Returns: Integer, number of results above the threshold
• Argument: none.
• Throws: none.
• Comments: none.
• See Also: THRESHOLD

🌟 pretty_print

• Title: pretty_print
• Usage: $output = $sig->pretty_print; / print $sig->pretty_print;
• Purpose: Emulates the output of the EGCG Sigcleave utility.
• Returns: A formatted string.
• Argument: none.
• Throws: none.
• Comments: none.
• See Also: n/a

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and that's the whole page bestie, no notes 💅✨

this one's brought to you by perl v5.32.1, dated 2021-08-15 — go forth and cleave those signal sequences, you absolute icon 🎀🦋💖