[BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
czmasek at burnham.org
Mon Jun 1 03:46:14 UTC 2009
In general only external nodes would have a sequence associated with them.
In the case of ancestral sequence reconstruction attempts, internal nodes might have sequences, too, though.
Please remember to none of the elements in phyloXML are mandatory.
With 'original' sequence I meant the sequence prior to alignment.
From: Michael Barton [mail at michaelbarton.me.uk]
Sent: Sunday, May 31, 2009 1:59 PM
To: Christian Zmasek
Cc: Phyloinformatics Group; bioruby at lists.open-bio.org; rozziite at gmail.com
Subject: Re: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
Would this mean that there is a predicted single ancestor sequence
object associated at each node in a phylogenetic tree? You could start
at a specific node and traverse to ancestor or descendant nodes, and
therefore sequences? When you write original sequence, you mean the
multiple sequence alignment?
2009/5/31 Christian Zmasek <czmasek at burnham.org>:
> Hi, Michael:
> Good point. Actually, it is not specified. It is just a sequence associated with a node.
> In my own work, I use it for the original sequence (before the introduction of gaps, and possible trimming of columns, during and after the alignment process).
> Hence, I do not think reuse of the MSA class is appropriate.
> From: bioruby-bounces at lists.open-bio.org [bioruby-bounces at lists.open-bio.org] On Behalf Of Michael Barton [mail at michaelbarton.me.uk]
> Sent: Sunday, May 31, 2009 2:45 AM
> To: Phyloinformatics Group; bioruby at lists.open-bio.org
> Subject: Re: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
> I'm not very familiar with phyloXML, but when you write sequence, do
> you mean a multiple sequence alignment from which the phylogeny was
> estimated? If that's the case, there is a MSA class in bioruby which
> this could be mapped to perhaps?
> 2009/5/30 Diana Jaunzeikare <rozziite at gmail.com>:
>> Hi all,
>> So I looked more carefully at the sequence element of phyloXML and it
>> consists of information which cannot be mapped to Bio::Sequence object. I
>> suggest to have a sequence class which closely resembles phyloXML structure
>> and then have a method to extract relevant elements return Bio::Sequence
>> object. What do you think?
>> Here on the left i listed phyloXML sequence tag elements and after the arrow
>> -> the possible corresponding attribute of Bio::Sequence
>> * type
>> ** rna, dna -> Bio::Sequence::NA -> molecule type
>> ** aa -> Bio::Sequence::AA
>> * id_source (string ?) -> id_namespace
>> * id_ref (string ) -> entry_id
>> * symbol (string ?)
>> * accession
>> ** source (example: "UniProtKB") ->
>> ** id (example: "P17304") -> primary_accession
>> * name (string )
>> * location (string ? )
>> * mol_seq (string) -> seq / Bio::Sequence::NA/AA
>> * uri
>> ** desc (string)
>> ** type (string )
>> ** uri
>> * annotation 
>> ** ref
>> ** source
>> ** evidence
>> ** type
>> ** desc
>> ** confidence
>> ** property 
>> ** uri
>> * domain_architecture
>> ** length
>> ** domain 
>> *** from
>> *** to
>> *** confidence
>> *** id
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