Re: [Seqan-dev] Annotation and spliced site

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

Hi Yue, 

thank you very much for writing us and sorry for keeping you on the loop for so long. 

I'd like you to raise such questions on the issue site on our github page: https://github.com/seqan/seqan/issues.

The mailing list is not-so-up-to-date anymore, and we will probably use this mailing list merely as a news feeder in the future to inform you about new releases or training courses.

Thank you very much for you understanding.

Kind regards,

René

On 14 Jun 2016, at 06:14, Yue Gan <gany.fml@gmail.com> wrote:

Hi all,

I am trying to use the annotation part of Seqan to solve a question, but I am a little bit confused.

What I want to do is to

1. Read in an annotation file (the format can be GFF, GTF, or BED)

2. Giving two positions (q1, q2) in the genome, decide if (q1, q2) is a known junction.

My Solution:

1. use GffFile in to load the annotation file(GFF, GTF) into a FragmentStore<>

2. extract the exons and create a junction Interval tree using the FragmentStore<>

3. using interval`s 'findIntervals' function giving q1 and q2 to find if there is an interval(junction) exists.

My Question:

1. Is BED better then GFF and GTF in this situation?

2. If BED is better, could anybody give me some examples what seqan data structure I should use to store and do the search? Some pseudocode with seqan data structure and function could be better....

3. If GFF and GTF are better, is my solution correct and efficient? Is there any better way to solve my question? Is there anything I need to pay attention to?

Thank you very much!

Yue Gan

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René Rahn

Ph.D. Student (de.NBI - CIBI)

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Tel:  (+49) 30 838 75137

Mail: rene.rahn@fu-berlin.de

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Institute of Computer Science

Algorithmic Bioinformatics (ABI)

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14195 Berlin

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