[BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence

[Michael Barton]

Hi Christian

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?

Cheers

Mike

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.
>
> 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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