Re: [Seqan-dev] Container type for storing sequences in memory

[Rahn, René <rene.maerker@fu-berlin.de>]

Hey, 

you are probably looking for a StringSet. 

This data structure simply stores a set of strings. You’ll need two of them for the ids and the sequences.

There is already functionality that directly reads a fasta file and stores the information in the StringSets.

You can read this tutorial to look into loading sequence files using StringSets.

http://seqan.readthedocs.org/en/develop/Tutorial/SequenceIO.html#tutorial-sequence-io

There you’ll also find links to the documentation of the StringSet.

Note that this is the current develop version. 

As we will have a release coming very soon this might be the thing to look at. 

cheers,

René

On 09 Jan 2015, at 11:00, Jordan Willis <jwillis0720@gmail.com> wrote:

Hi,

I was wondering if there is a builtin container in Seqan for storing a small database of sequence ids and sequences that can be stored in memory. The sequences will be continually iterated through and local alignments will be performed. Does anyone have any recommendations for this or perhaps point me to one of the builtin apps that does this?

Thanks so much,
j
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René Rahn

Ph.D. Student

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Tel:  (+49) 30 838 75277

Mail: rene.rahn@fu-berlin.de

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Institute of Computer Science

Algorithmic Bioinformatics (ABI)

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Freie Universität Berlin

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14195 Berlin

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