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ACE::SEQUENCE::HOMOL(3PM) - Linux man page online | Library functions

Temporary Sequence Homology Class.

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2017-11-24
Ace::Sequence::Homol(3pm) User Contributed Perl Documentation Ace::Sequence::Homol(3pm)

NAME

Ace::Sequence::Homol - Temporary Sequence Homology Class

SYNOPSIS

# Get all similarity features from an Ace::Sequence @homol = $seq->features('Similarity'); # sort by score @sorted = sort { $a->score <=> $b->score } @homol; # the last one has the highest score $best = $sorted[$#sorted]; # fetch its associated Ace::Sequence::Homol $homol = $best->target; # print out the sequence name, DNA, start and end print $homol->name,' ',$homol->start,'-',$homol->end,"\n"; print $homol->asDNA;

DESCRIPTION

Ace::Sequence::Homol is a subclass of Ace::Object (not Ace::Sequence) which is specialized for returning information about a DNA or protein homology. This is a temporary placeholder for a more sophisticated homology class which will include support for alignments.

OBJECT CREATION

You will not ordinarily create an Ace::Sequence::Homol object directly. Instead, objects will be created in response to an info() or group() method call on a similarity feature in an Ace::Sequence::Feature object. If you wish to create an Ace::Sequence::Homol object directly, please consult the source code for the new() method.

OBJECT METHODS

Most methods are inherited from Ace::Object. The following methods are also supported: start() $start = $homol->start; Returns the start of the area that is similar to the Ace::Sequence::Feature from which his homology was derived. Coordinates are relative to the target homology. end() $end = $homol->end; Returns the end of the area that is similar to the Ace::Sequence::Feature from which his homology was derived. Coordinates are relative to the target homology. asString() $label = $homol->asString; Returns a human-readable identifier describing the nature of the feature. The format is: $name/$start-$end for example: HUMGEN13/1-67 This method is also called automatically when the object is treated in a string context.

SEE ALSO

Ace, Ace::Object, Ace::Sequence,Ace::Sequence::FeatureList, Ace::Sequence::Feature, GFF

AUTHOR

Lincoln Stein <@w3.org> with extensive help from Jean Thierry-Mieg <@kaa.crbm.cnrs-mop.fr> Copyright (c) 1999, Lincoln D. Stein This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.
perl v5.26.1 2017-11-24 Ace::Sequence::Homol(3pm)
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