Bio::Chaos::FeatureUtil - sequence and feature utilities
Bio::Chaos::FeatureUtil->blah('xx');
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).
(bmin, bmax, strand)
base coordinates with minmax semantics - native to bioperl
(imin, imax, strand)
interbase with minmax semantics - native to chado
(nbeg, nend, ?strand)
interbase vector (in the mathematical sense)
so called natural begin and end - this is the native chaos coordinate system