[BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence

[Christian Zmasek]

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.

Christian

 


________________________________________
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
>
> Diana
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> BioRuby at lists.open-bio.org
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>

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