[Biopython-dev] [Biopython - Feature #3388] add annotation and letter_annotations attributed for Bio.Align.MultipleSeqAlignment. object

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Issue #3388 has been updated by Peter Cock.


Support for a generic annotation dictionary done,
https://github.com/biopython/biopython/commit/793f9210696e0acc9606faeca3d6ca47a9d97813

Started work on per-column annotation as well - currently on this branch:
https://github.com/peterjc/biopython/tree/per-column-annotation

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Feature #3388: add annotation and letter_annotations attributed for Bio.Align.MultipleSeqAlignment. object
https://redmine.open-bio.org/issues/3388

Author: saverio vicario
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


At the moment I could not add annotation at alignment level.  annotation could be usefull for tracking info linked to the loci ( i.e. name of domain), while letter annotation could be usefull to track quality score of alignment or if the sites belong to a given character set.
In particular when to alignment are merged it would be usefull tha the bounduary of the merge is tracked
for example in Letter annotation of the merge of an alignment a with 10 sites and b of 5 sites the letter_annotations would be as following 

{locus1:'111111111100000',locus2:'000000000011111'} 
this could be usefull also to annotate the 3 position of codons
{pos1:'1001001001',pos2:'0100100100', pos3:'0010010010'}

If this letter_annotation would be supported the annotation could be kept across merging and splitting of the alignment


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