[Bioperl-l] LiveSeq

Joseph Insana insana@ebi.ac.uk
Fri, 16 Feb 2001 13:41:36 +0000 (GMT)

> In looking through the different modules I came acros Bio::LiveSeq. Is
> this used heavily

Right now it's used only by Heikki and me (the coders).

> how does this interface with (Primary)Seq

LiveSeq is designed to be quite independent from the other BioPerl modules.
One of its loader modules (in IO subdir) is SRS.pm that takes advantage
of a local srs installation (or a corba one with some minor tweaks) to
parse embl and swissprot, without passing through bioperl.

> the code, it's a reimplementation

It's a reimplementation with a totally different concept (that of relying on
hanldes on single nucleotides instead than positions in any arbitrary
sequence-based coordinate system). This makes it very easy to deal with
mutations, even very complex ones without having to bother keeping in sync
the coordinate system.

> example code, but don't get much wiser from the docs.

The methods are near all commented but I agree that getting a whole picture
is somewhat difficult. Write to me if you have specific questions.

Joseph Insana