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Bio::Chaos::FeatureUtil - sequence and feature utilities

Bio::Chaos::FeatureUtil - sequence and feature utilities


NAME


  Bio::Chaos::FeatureUtil     - sequence and feature utilities


SYNOPSIS


  Bio::Chaos::FeatureUtil->blah('xx');


DESCRIPTION

COORDINATES

Coordinates are either Interbase or <Base-oriented>.

Interbase coordinates count the spaces between bases and the origin is zero

Base-oriented coordinates count the bases and the origin is 1

To convert between these two, add/subtract 1 from the minimum (low) coordinate only

Imagine a sequence TCATGCAA eg 1 2 3 4 5 6 7 8 BASE T C A T G C A A 0 1 2 3 4 5 6 7 8 INTERBASE

In interbase, the ATG codon is [2,5]; in base it is [3,5]

With interbase, length is high-low

With base, length is (high-low)+1

interbase has the advantages of simpler arithmetic, and the ability to represent length-zero features (eg insertions)

Beyond the base/interbase distinction, ranges can also be specified as either min-max-strand triples (directionality explicit) or begin-end pairs (directionality implicit).

bcmm

  (bmin, bmax, strand)

base coordinates with minmax semantics - native to bioperl

ibmm

  (imin, imax, strand)

interbase with minmax semantics - native to chado

ibv

  (nbeg, nend, ?strand)

interbase vector (in the mathematical sense)

so called natural begin and end - this is the native chaos coordinate system

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