Storing BLAST results in Chado

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Storing BLAST results in Chado

ganeshS
Hello Scott and Members

Thanks you for the prompt and very informative responses!

Our group is considering using Chado's schema and tools for storing BLAST results.

I have some concerns and questions, regarding this..

I see some of the Blast result captured in the AnalysisFeature table. Ideally it would be great to be able to store information like 'Match Length', "Number of Identicals", "Number of Positives", "Reading Frame of the match"  that the blast results file provides.

I don't see these captured directly by schema (esp for pre-stored features like a Gene, I don't see and easy way of deducing the alignment length of match as the sequence length in Feature tables is that of the whole gene).

I am assuming we will have to add a table to capture these if we decide to use Chado and then a tool to load these values in to the proper table.

Any advice/suggestion for such a scenario would be great!

Thanks
Ganesh

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Re: Storing BLAST results in Chado

Siddhartha Basu
Hi,

On Tue, 30 Apr 2013, Srinivasamoorthy, Ganesh - INTL wrote:

>    Hello Scott and Members
>
>    Thanks you for the prompt and very informative responses!
>
>    Our group is considering using Chado's schema and tools for storing BLAST
>    results.
>
>    I have some concerns and questions, regarding this..
>
>    I see some of the Blast result captured in the AnalysisFeature table.
>    Ideally it would be great to be able to store information like 'Match
>    Length', "Number of Identicals", "Number of Positives", "Reading Frame of
>    the match"  that the blast results file provides.
>
>    I don't see these captured directly by schema (esp for pre-stored features
>    like a Gene, I don't see and easy way of deducing the alignment length of
>    match as the sequence length in Feature tables is that of the whole gene).
The HSP in feature table should have a pair of featureloc, one for query
and one for subject. You could use that to deduce the length of
alignment. You might also use the *seqlen* column in feature table if
you prefer. Also have a look here for details
http://gmod.org/wiki/Chado_Companalysis_Module if you haven't already
done so.

>
>    I am assuming we will have to add a table to capture these if we decide to
>    use Chado and then a tool to load these values in to the proper table.
Yes, the analysisfeature table provides rather few columns for storing
alignment information. To add additional table to store arbitary/custom
alignment information(key value style), look at the design of various chado
props table, for example featureprop, should give you some idea for a
new table.
As an alternative, you could also add a hstore column to analysisfeature
for storing any alignment information(key value style) that is not
provided by default.
http://www.postgresql.org/docs/9.2/static/hstore.html

Hope this helps,
-siddhartha


>
>    Any advice/suggestion for such a scenario would be great!
>
>    Thanks
>    Ganesh

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Re: Storing BLAST results in Chado

Scott Cain
Hi Ganesh,

You can store as much information as you want related to individual results in analysisfeatureprop as key value pairs.

Scott



On Wed, May 1, 2013 at 12:23 PM, Siddhartha Basu <[hidden email]> wrote:
Hi,

On Tue, 30 Apr 2013, Srinivasamoorthy, Ganesh - INTL wrote:

>    Hello Scott and Members
>
>    Thanks you for the prompt and very informative responses!
>
>    Our group is considering using Chado's schema and tools for storing BLAST
>    results.
>
>    I have some concerns and questions, regarding this..
>
>    I see some of the Blast result captured in the AnalysisFeature table.
>    Ideally it would be great to be able to store information like 'Match
>    Length', "Number of Identicals", "Number of Positives", "Reading Frame of
>    the match"  that the blast results file provides.
>
>    I don't see these captured directly by schema (esp for pre-stored features
>    like a Gene, I don't see and easy way of deducing the alignment length of
>    match as the sequence length in Feature tables is that of the whole gene).
The HSP in feature table should have a pair of featureloc, one for query
and one for subject. You could use that to deduce the length of
alignment. You might also use the *seqlen* column in feature table if
you prefer. Also have a look here for details
http://gmod.org/wiki/Chado_Companalysis_Module if you haven't already
done so.

>
>    I am assuming we will have to add a table to capture these if we decide to
>    use Chado and then a tool to load these values in to the proper table.
Yes, the analysisfeature table provides rather few columns for storing
alignment information. To add additional table to store arbitary/custom
alignment information(key value style), look at the design of various chado
props table, for example featureprop, should give you some idea for a
new table.
As an alternative, you could also add a hstore column to analysisfeature
for storing any alignment information(key value style) that is not
provided by default.
http://www.postgresql.org/docs/9.2/static/hstore.html

Hope this helps,
-siddhartha


>
>    Any advice/suggestion for such a scenario would be great!
>
>    Thanks
>    Ganesh

> ------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1

> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
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--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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