[Bioperl-l] additional methods for Bio::SeqUtils for in-silico cloning

Roy Chaudhuri roy.chaudhuri at gmail.com
Tue Jan 10 10:25:09 EST 2012

Hi Frank,

Looks good to me. One thing I'm not sure about - why do features 
overlapping a deletion become fuzzy? That behaviour is in 
trunc_with_features because it's intended to represent a taking a 
subregion of a larger sequence, but if you're representing an internal 
deletion then the boundaries of the overlapping feature aren't unknown, 
they have been specifically altered. Maybe you could give absolute 
coordinates, but add a note indicating that the 5' or 3' end has been 
truncated by however many bases.


On 10/01/2012 13:10, Frank Schwach wrote:
> Hi Chris,
> I have made the changes in a Git fork and made the pull request now.
> If this is accepted into BioPerl I can also write a little SeqUtils
> HOWTO for the BioPerl wiki.
> Frank
> On Mon, 2012-01-09 at 18:29 +0000, Fields, Christopher J wrote:
>> Sounds very promising!  The easiest way to contribute is via a fork of the code on Github with a pull request (as you already know, being a contributor to the Primer3 modules).
>> chris
>> On Jan 9, 2012, at 11:10 AM, Frank Schwach wrote:
>>> Hi all,
>>> I needed to manipulate Bio::Seq objects with annotations and sequence
>>> features to simulate molecular cloning techniques, e.g. to cut a vector
>>> and insert a fragment into it while preserving all the annotations and
>>> moving the features accordingly.
>>> My main aim was to split features that span deletion/insertion sites in
>>> a meaningful way, which can not be done with the currently availble
>>> methods.
>>> I have modified Bio::SeqUtils so that I have the following new methods:
>>> delete
>>> ======
>>> removes a segment from a sequence object and adjusts positions and types
>>> of locations of sequence features:
>>> - locations of features that span the deletion sites are turned into
>>> Splits.
>>> - locations that extend into the deleted region are turned to Fuzzy to
>>> indicate that their true start/end was lost.
>>> - locations contained inside the deleted regions are lost.
>>> - other features are shifted according to the length of the deletion.
>>> insert
>>> ======
>>> adds a Bio::Seq object into another one between specified insertion
>>> sites. This also affects the features on the recipient sequence:
>>> - locations of features that span the insertion site are split but
>>> position types are not turned to Fuzzy because no part of the original
>>> feature is lost.
>>> - other features are shifted according to the length of the insertion.
>>> ligate
>>> ======
>>> just for convenience. Supply a recipient, a fragment and one or two
>>> sites to cut the recipient. Can also flip the fragment if required.
>>> Simply calls delete [, reverse_complement_with_features] and insert in
>>> turn.
>>> One situation I haven't handled yet is a deletion that spans the origin
>>> of a circular molecule but that should be a rare thing to do anyway. The
>>> code currently throws an error if this is attempted.
>>> I'm happy to contribute the code on Github if there is interest?
>>> Comments on the handling of feature locations highly welcome!
>>> Frank

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