[ensembl-dev] [SPAM] - Re: [SPAM] - Re: [SPAM] - Re: [SPAM] - Re: Transcript variation alleles - Email found in subject - Email found in subject - Email found in subject - Email found in subject

[Oliver, Gavin]

Thanks again Will!

 

 

 

________________________________

From: wmclaren at gmail.com [mailto:wmclaren at gmail.com] On Behalf Of Will
McLaren
Sent: 02 February 2011 16:32
To: Oliver, Gavin
Cc: Graham Ritchie; dev at ensembl.org
Subject: [SPAM] - Re: [SPAM] - Re: [SPAM] - Re: [SPAM] - Re:
[ensembl-dev] Transcript variation alleles - Email found in subject -
Email found in subject - Email found in subject - Email found in subject

 

A variation is defined by its alleles and a pair of flanking sequence,
e.g.:

 

ATCGTACTGTACGTGTTTATCG [A/G] TGACTTACTATCGTATGACTT

 

dbSNP (or in some cases Ensembl) use sequence alignment algorithms to
map this sequence to the genomic reference sequence. If it maps to the
reverse strand, we create a variation_feature on the reverse strand. In
some cases the sequence may map more than once, hence a variation object
can have multiple associated variation_feature objects. This is easier
to see on the web views:

 

http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=rs78197743;vdb=v
ariation

 

As I mentioned, it makes our lives easier if most things are on the
forward strand, so we "flip" as many of these reverse strand mappings as
we can. We only do this when a variation has a single mapping to the
reverse strand.

 

Will

On 2 February 2011 16:17, Oliver, Gavin <gavin.oliver at almacgroup.com>
wrote:

Cool, thanks.

 

What determines the strand it goes on?

 

________________________________

 


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