Re: [Seqan-dev] about extendSeed of Seqan

["Kehr, Birte" <Birte.Kehr@fu-berlin.de>]

Hi Beifang,

the function extendSeed does not return the number of matched sequence positions.

I assume you have used ungapped X-drop extension? Then you can count matching positions by simply iterating over the infixes:

typedef typename Infix<TSeq>::Type TInfix;
TInfix infix1 = infix(seq1, leftPosition(seed, 0), rightPosition(seed, 0)+1);
TInfix infix2 = infix(seq2, leftPosition(seed, 1), rightPosition(seed, 1)+1);

unsigned count = 0;
for(int i = 0; i < length(seed); ++i)
{
    if (value(infix1, i) == value(infix2, i))
        ++count;
}

-Birte

________________________________________
From: Beifang Niu [neilniu.cn@gmail.com]
Sent: Thursday, October 27, 2011 9:19 PM
To: Kehr, Birte
Subject: Re: seqan-dev Digest, Vol 25, Issue 6

Hi Birte,

Thank you for your prompt response but I didn't receive your reply from seqan development mail list.
 I did see the example for seed extension in the SeqAn-Tutorial. Now, I have other questions for you.
 How can I get the actual aligned bases number between two extended seeds after running extendSeeds?
 for example, sequences: ACGTAGTTT  and ACGTGGTTT , there is one seed GTTT, after the extension of left , I got the extension seeds:     ACGTAGTTT   and ACGTGGTTT ( there is only one mismatch) , the actual aligned bases number is  8.
 I want to get this number but I don;t know how to get it only running extendSeeds.



thank you,
Beifang.

On Tue, Oct 25, 2011 at 3:00 AM, <seqan-dev-request@lists.fu-berlin.de<mailto:seqan-dev-request@lists.fu-berlin.de>> wrote:
Send seqan-dev mailing list submissions to
       seqan-dev@lists.fu-berlin.de<mailto:seqan-dev@lists.fu-berlin.de>

To subscribe or unsubscribe via the World Wide Web, visit
       https://lists.fu-berlin.de/listinfo/seqan-dev
or, via email, send a message with subject or body 'help' to
       seqan-dev-request@lists.fu-berlin.de<mailto:seqan-dev-request@lists.fu-berlin.de>

You can reach the person managing the list at
       seqan-dev-owner@lists.fu-berlin.de<mailto:seqan-dev-owner@lists.fu-berlin.de>

When replying, please edit your Subject line so it is more specific
than "Re: Contents of seqan-dev digest..."


Today's Topics:

  1. about extendSeed of Seqan (Beifang Niu)
  2. Re: about extendSeed of Seqan (Kehr, Birte)


----------------------------------------------------------------------

Message: 1
Date: Mon, 24 Oct 2011 14:50:33 -0700
From: Beifang Niu <neilniu.cn@gmail.com<mailto:neilniu.cn@gmail.com>>
Subject: [Seqan-dev] about extendSeed of Seqan
To: seqan-dev@lists.fu-berlin.de<mailto:seqan-dev@lists.fu-berlin.de>
Message-ID:
       <CABnPkb9P5nAvhQD_4in6mo+Vtim6uhjWEFgzGMhxfb5XWuLQ2g@mail.gmail.com<mailto:CABnPkb9P5nAvhQD_4in6mo%2BVtim6uhjWEFgzGMhxfb5XWuLQ2g@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"

Hi,

I am trying to use Seqan library to do the MEM (max exact match) extension.
Firstly, I get the MEM of the two genome sequences using MUMMER3 and then I
want to use extendSeed of Seqan to do extension of MEMs.
Is there any examples for extendSeed function of seeds class?

thanks,
Beifang.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.fu-berlin.de/pipermail/seqan-dev/attachments/20111024/bca37918/attachment.htm>

------------------------------

Message: 2
Date: Tue, 25 Oct 2011 00:59:24 +0200
From: "Kehr, Birte" <Birte.Kehr@fu-berlin.de<mailto:Birte.Kehr@fu-berlin.de>>
Subject: Re: [Seqan-dev] about extendSeed of Seqan
To: SeqAn Development <seqan-dev@lists.fu-berlin.de<mailto:seqan-dev@lists.fu-berlin.de>>
Message-ID:
       <DAD226CB6878494EABEFD5215AA102015A8DE1CD68@exchange6.fu-berlin.de<DAD226CB6878494EABEFD5215AA102015A8DE1CD68@exchange6.fu-berlin.de">mailto:DAD226CB6878494EABEFD5215AA102015A8DE1CD68@exchange6.fu-berlin.de>>
Content-Type: text/plain; charset="us-ascii"

Hi Beifang,

you can find an example for seed extension in the SeqAn-Tutorial at
http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/Seed-and-Extend#SeedExtensionAndBandedAlignment.

You might also want to consider to use the seeds2 module instead of the seeds module since we plan to replace the seeds module by the seeds2 module. Unfortunately, there is no example on how to use the seeds2 module, yet.

-Birte


From: Beifang Niu [mailto:neilniu.cn@gmail.com<mailto:neilniu.cn@gmail.com>]
Sent: Montag, 24. Oktober 2011 14:51
To: seqan-dev@lists.fu-berlin.de<mailto:seqan-dev@lists.fu-berlin.de>
Subject: [Seqan-dev] about extendSeed of Seqan

Hi,

I am trying to use Seqan library to do the MEM (max exact match) extension.
Firstly, I get the MEM of the two genome sequences using MUMMER3 and then I want to use extendSeed of Seqan to do extension of MEMs.
Is there any examples for extendSeed function of seeds class?

thanks,
Beifang.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.fu-berlin.de/pipermail/seqan-dev/attachments/20111025/a7b787b0/attachment.htm>

------------------------------

_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de<mailto:seqan-dev@lists.fu-berlin.de>
https://lists.fu-berlin.de/listinfo/seqan-dev


End of seqan-dev Digest, Vol 25, Issue 6
****************************************