[Biococoa-dev] Reading blast formatted files

[Davide Cittaro]

Hi Koen
On Aug 10, 2006, at 6:34 PM, Koen van der Drift wrote:

> Hi Davide,
>
> Welcome to BioCocoa! It would be great if the framework will be  
> used in a proteomics app.

Well, I have some ideas but, as I said, I'm pretty new to Cocoa  
programming, so you have to give me time to understand a lot of  
things... :-)

> What I understand, formatdb is a standalone CLI app, correct? We  
> need to look into if we can add this (because of possible license  
> issues). Otherwise, we can write our own class, based on the  
> formatdb source code. I encourage you to look into that  
> possibility, we can help here to convert it to Objective-C and Cocoa.

I'm thinking about reading the code of fastacmd utility instead of  
formatdb, as fastacmd does read blast formatted databases and can  
extract some info (whole sequences, accession numbers only, get only  
a sequence or the entire database...). I'll take a look then to the  
source code, then

d


>
> cheers,
>
> - Koen.
>
>
>
> -----Original Message-----
>> From: Davide Cittaro <davide.cittaro at ifom-ieo-campus.it>
>> Sent: Aug 10, 2006 11:32 AM
>> To: BioCocoa Mailinglist <biococoa-dev at bioinformatics.org>
>> Subject: [Biococoa-dev] Reading blast formatted files
>>
>> Hi there, I'm new to BioCocoa (well, I've discovered it yesterday)
>> and pretty new to Cocoa programming. I would like to start using this
>> framework for some proteomics app.
>> I would like to know if there is a way to read database formatted for
>> NCBI blast with formatdb. Ok, I'm also going to read the  
>> documentation!
>>
>> d
>> /*
>> Davide Cittaro
>> HPC and Bioinformatics Systems @ Informatics Core
>>
>> IFOM - Istituto FIRC di Oncologia Molecolare
>> via adamello, 16
>> 20139 Milano
>> Italy
>>
>> tel.: +39(02)574303355
>> e-mail: davide.cittaro at ifom-ieo-campus.it
>> */
>>
>>
>>
>
>
>

/*
Davide Cittaro
HPC and Bioinformatics Systems @ Informatics Core

IFOM - Istituto FIRC di Oncologia Molecolare
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303355
e-mail: davide.cittaro at ifom-ieo-campus.it
*/



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