From laeciofreitas@gmail.com Tue Jan 21 17:05:45 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1W5dpf-0038fT-Nf>; Tue, 21 Jan 2014 17:05:44 +0100 Received: from mail-lb0-f179.google.com ([209.85.217.179]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1W5dpf-0018Ai-Km>; Tue, 21 Jan 2014 17:05:43 +0100 Received: by mail-lb0-f179.google.com with SMTP id l4so4397527lbv.24 for ; Tue, 21 Jan 2014 08:05:42 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:from:date:message-id:subject:to:content-type; bh=mi7VZRWaP5eujofSEpmvfexUXC2X5Cd9wMNJaRecTDc=; b=1Dx0dT+Kapabrvo7ViNwv3q6bUShcIAO3sbldgPFRkIzWrA59OEmtFzDYthmE1Rn8t O4ssms9zEpCq48ox/FUMB30DsZsgvNjQfrBXA8xFH7PJU2I3nKivm7HxwJNn9rv0c9Up 3HgtYAjuGVA9v5XmQ5bAVa+zDECtvG/bdEN6DcDgTSORt0iNSpgbUzCHxR26TMuROyrk qpzsUvv5o7FCgMBJq3zGyGqQobYF1aP5yVseqkYeGA8mFbMkAcThz633v80647bGX1AB LaNlCvpNWMv7EMZ/V3ayBLtlF40jlMrNQCtnEBF9IF5ZZMzS0zAZMZ+vSBlKDyT84neW OexQ== X-Received: by 10.112.164.35 with SMTP id yn3mr1996349lbb.45.1390320342181; Tue, 21 Jan 2014 08:05:42 -0800 (PST) MIME-Version: 1.0 Received: by 10.114.169.226 with HTTP; Tue, 21 Jan 2014 08:05:22 -0800 (PST) From: =?ISO-8859-1?Q?La=E9cio_Freitas_Chaves?= Date: Tue, 21 Jan 2014 14:05:22 -0200 Message-ID: To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=001a11c335301eb0f004f07d2ef9 X-Originating-IP: 209.85.217.179 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1390320343-0000CD40-90C5258B/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.002075, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.5 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, HTML_OBFUSCATE_10_20,RCVD_IN_DNSWL_LOW,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Segments with gaps X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 21 Jan 2014 16:05:45 -0000 --001a11c335301eb0f004f07d2ef9 Content-Type: text/plain; charset=ISO-8859-1 Hi, A question: the SeqAn aligns segments matches with gaps? --001a11c335301eb0f004f07d2ef9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hi,

A question: the=A0SeqAn=A0aligns segments mat= ches with gaps?

--001a11c335301eb0f004f07d2ef9-- From manuel.holtgrewe@fu-berlin.de Tue Jan 21 17:10:28 2014 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1W5duE-003A9E-QZ>; Tue, 21 Jan 2014 17:10:26 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1W5duE-0049e5-Nx>; Tue, 21 Jan 2014 17:10:26 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1W5duE-002Vvy-9c>; Tue, 21 Jan 2014 17:10:26 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0174.001; Tue, 21 Jan 2014 17:10:25 +0100 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] Segments with gaps Thread-Index: AQHPFsKoofW4XoO2N02kJ/e1m54+ZpqPWPod Message-ID: References: In-Reply-To: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_FCCAB9D80C3DAB47B5601C5B0E62872B915EDF2Fex02acampusfube_" MIME-Version: 1.0 Date: Tue, 21 Jan 2014 17:10:23 +0100 X-Original-Date: Tue, 21 Jan 2014 16:10:23 +0000 X-Originating-IP: 130.133.170.203 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1390320626-0000CD40-644F4D2B/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Segments with gaps X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 21 Jan 2014 16:10:28 -0000 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B915EDF2Fex02acampusfube_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Laecio, could you make your question more specific and elaborate a bit? Cheers, Manuel ________________________________ From: La=E9cio Freitas Chaves [laeciofreitas@gmail.com] Sent: Tuesday, January 21, 2014 5:05 PM To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] Segments with gaps Hi, A question: the SeqAn aligns segments matches with gaps? --_000_FCCAB9D80C3DAB47B5601C5B0E62872B915EDF2Fex02acampusfube_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear Laecio,

could you make your question more specific and elaborate a bit?

Cheers,

Manuel

From: La=E9cio Freitas Chaves [laeciofrei= tas@gmail.com]
Sent: Tuesday, January 21, 2014 5:05 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Segments with gaps

Hi,

A question: t<= /span>he = SeqAn aligns segments matches with gaps?

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

--=_12AAB9F7-064C-4FD0-9366-340DFFC68EFD-- --=_47C7EF4B-2C35-4FBE-885F-8AB5F05EC4B6-- From birte.kehr@fu-berlin.de Thu Jan 23 09:36:40 2014 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1W6FmA-0001ZT-R1>; Thu, 23 Jan 2014 09:36:38 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1W6FmA-000BOP-OV>; Thu, 23 Jan 2014 09:36:38 +0100 Received: from [213.190.120.95] (helo=[192.168.1.147]) by inpost2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1W6Fm9-001NwT-Ux>; Thu, 23 Jan 2014 09:36:38 +0100 Message-ID: <52E0D487.8040103@fu-berlin.de> Date: Thu, 23 Jan 2014 08:36:23 +0000 From: Birte Kehr User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:24.0) Gecko/20100101 Thunderbird/24.2.0 MIME-Version: 1.0 To: SeqAn Development References: <91327B90-F9F4-4EF2-AA69-91A66E3B8B6D@gmail.com> <62D80583-7B65-4D88-A124-6E58F0AD8DF9@gmail.com> In-Reply-To: <62D80583-7B65-4D88-A124-6E58F0AD8DF9@gmail.com> Content-Type: multipart/alternative; boundary="------------070805010907080202050905" X-Originating-IP: 213.190.120.95 X-ZEDAT-Hint: A X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1390466198-0000CD40-CC72FE04/1/4085811623 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-49.0 required=5.0 tests=ALL_TRUSTED, FU_XPURGATE_SUSP, HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Disallowing gaps in an alignment X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 23 Jan 2014 08:36:40 -0000 This is a multi-part message in MIME format. --------------070805010907080202050905 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi, is the following one possibility of what you want your alignment to look like? ----CDFH-------- | CAAAADAAAAFAAAAH Then you should try passing AlignConfig() as an additional parameter to the globalAlignment function. This will not add gap penalties for leading and trailing gaps in the first sequence. http://docs.seqan.de/seqan/dev3/?p=AlignConfig http://docs.seqan.de/seqan/dev3/?p=globalAlignment Birte Am 23.01.2014 08:19, schrieb Karrde: > Sorry if you got this twice, I just realized I accidentally hit reply > instead of reply-all. > > First off, thanks for the response. > > I tried your idea but I'm not getting the correct results, I still see > several gaps in the alignment. I also tried setting the gap-extend to > a high cost while leaving gap-open at 0, but this doesn't actually > seem to do anything to the score returned. > > Here's the code I used: > > TSequence seq1 = "CDFH"; > TSequence seq2 = "CAAAADAAAAFAAAAH"; > > TAlign align; > resize(rows(align), 2); > assignSource(row(align,0),seq1); > assignSource(row(align,1),seq2); > > //trying to set the gap penalty extra high > seqan::Score seqan::Blosum62_>> scoreRoutine(-100,0); > > Output from scoreRoutine(-100,0) > Score: 27 > 0 . : . > C----D----F----H > | | | | > CAAAADAAAAFAAAAH > > Output from scoreRoutine(-100,-100) > Score: -1173 > 0 . : . > C----D----F----H > | | | | > CAAAADAAAAFAAAAH > > > > > >> On Jan 23, 2014, at 1:10 AM, Holtgrewe, Manuel >> wrote: >> >> Hi, simply use very high gap costs in the constructor. >> >> http://docs.seqan.de/seqan/dev3/?p=MatrixScore#Score >> >> *m >> >> ________________________________ >> From: Karrde [karrde.dev@gmail.com] >> Sent: Wednesday, January 22, 2014 11:48 PM >> To: seqan-dev@lists.fu-berlin.de >> Subject: [Seqan-dev] Disallowing gaps in an alignment >> >> Hello, >> >> I want to perform an alignment such that there are no gaps allowed >> using the Blosum62 mutation matrix. In practice, one of my sequences >> will be much smaller than the other. I want it to align as close as >> possible to the longer sequence without allowing any gaps. Is there a >> flag or something I can set to disallow any gaps or set the maximum >> number of gaps allowed? >> >> I'm new to SeQan, but here's what I have so far (test data): >> >> typedef seqan::String TSequence; >> typedef seqan::Align TAlign; >> >> TSequence seq1 = "CDFGAAAHC"; >> TSequence seq2 = "CDEFGAHC"; >> >> TAlign align; >> resize(rows(align), 2); >> assignSource(row(align,0),seq1); >> assignSource(row(align,1),seq2); >> >> double score = globalAlignment(align, seqan::Score> seqan::ScoreMatrix>()); >> std::cout << "Score: " << score << ::std::endl; >> std::cout << align << ::std::endl; >> >> Thanks for any and all help! >> >> Hi, simply use very high gap costs in the constructor. >> >> http://docs.seqan.de/seqan/dev3/?p=MatrixScore#Score >> >> *m >> >> ------------------------------------------------------------------------ >> *From:* Karrde [karrde.dev@gmail.com] >> *Sent:* Wednesday, January 22, 2014 11:48 PM >> *To:* seqan-dev@lists.fu-berlin.de >> *Subject:* [Seqan-dev] Disallowing gaps in an alignment >> >> Hello, >> >> I want to perform an alignment such that there are no gaps allowed >> using the Blosum62 mutation matrix. In practice, one of my sequences >> will be much smaller than the other. I want it to align as close as >> possible to the longer sequence without allowing any gaps. Is there a >> flag or something I can set to disallow any gaps or set the maximum >> number of gaps allowed? >> >> I'm new to SeQan, but here's what I have so far (test data): >> >> typedef seqan::String TSequence; >> typedef seqan::Align TAlign; >> >> TSequence seq1 = "CDFGAAAHC"; >> TSequence seq2 = "CDEFGAHC"; >> >> TAlign align; >> resize(rows(align), 2); >> assignSource(row(align,0),seq1); >> assignSource(row(align,1),seq2); >> >> double score = globalAlignment(align, seqan::Score> seqan::ScoreMatrix>()); >> std::cout << "Score: " << score << ::std::endl; >> std::cout << align << ::std::endl; >> >> Thanks for any and all help! >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev >> > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --------------070805010907080202050905 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, is the following one possibility of what you want your alignment to look like?

----CDFH--------

CAAAADAAAAFAAAAH

Then you should try passing AlignConfig<false, true, true, false>() as an additional parameter to the globalAlignment function. This will not add gap penalties for leading and trailing gaps in the first sequence.

http://docs.seqan.de/seqan/dev3/?p=AlignConfig

http://docs.seqan.de/seqan/dev3/?p=globalAlignment

Birte

Am 23.01.2014 08:19, schrieb Karrde:

Sorry if you got this twice, I just realized I accidentally hit reply instead of reply-all.

First off, thanks for the response.

I tried your idea but I'm not getting the correct results, I still see several gaps in the alignment. I also tried setting the gap-extend to a high cost while leaving gap-open at 0, but this doesn't actually seem to do anything to the score returned.

Here's the code I used:

TSequence seq1 = "CDFH";

TSequence seq2 = "CAAAADAAAAFAAAAH";

TAlign align;

resize(rows(align), 2);

assignSource(row(align,0),seq1);

assignSource(row(align,1),seq2);

//trying to set the gap penalty extra high

seqan::Score<int, seqan::ScoreMatrix<seqan::AminoAcid, seqan::Blosum62_>> scoreRoutine(-100,0);

Output from scoreRoutine(-100,0)

Score: 27

0 . : .

C----D----F----H

| | | |

CAAAADAAAAFAAAAH

Output from scoreRoutine(-100,-100)

Score: -1173

0 . : .

C----D----F----H

| | | |

CAAAADAAAAFAAAAH

On Jan 23, 2014, at 1:10 AM, Holtgrewe, Manuel <manuel.holtgrewe@fu-berlin.de> wrote:

Hi, simply use very high gap costs in the constructor.

http://docs.seqan.de/seqan/dev3/?p=MatrixScore#Score

*m

________________________________
From: Karrde [karrde.dev@gmail.com]
Sent: Wednesday, January 22, 2014 11:48 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Disallowing gaps in an alignment

Hello,

I want to perform an alignment such that there are no gaps allowed using the Blosum62 mutation matrix. In practice, one of my sequences will be much smaller than the other. I want it to align as close as possible to the longer sequence without allowing any gaps. Is there a flag or something I can set to disallow any gaps or set the maximum number of gaps allowed?

I'm new to SeQan, but here's what I have so far (test data):

typedef seqan::String<char> TSequence;
typedef seqan::Align<TSequence,seqan::ArrayGaps> TAlign;

TSequence seq1 = "CDFGAAAHC";
TSequence seq2 = "CDEFGAHC";

TAlign align;
resize(rows(align), 2);
assignSource(row(align,0),seq1);
assignSource(row(align,1),seq2);

double score = globalAlignment(align, seqan::Score<int, seqan::ScoreMatrix<seqan::AminoAcid, seqan::Blosum62_>>());
std::cout << "Score: " << score << ::std::endl;
std::cout << align << ::std::endl;

Thanks for any and all help!

Hi, simply use very high gap costs in the constructor.

http://docs.seqan.de/seqan/dev3/?p=MatrixScore#Score

*m

From: Karrde [karrde.dev@gmail.com]
Sent: Wednesday, January 22, 2014 11:48 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Disallowing gaps in an alignment

Hello,

I want to perform an alignment such that there are no gaps allowed using the Blosum62 mutation matrix. In practice, one of my sequences will be much smaller than the other. I want it to align as close as possible to the longer sequence without allowing any gaps. Is there a flag or something I can set to disallow any gaps or set the maximum number of gaps allowed?

I'm new to SeQan, but here's what I have so far (test data):

typedef seqan::String<char> TSequence;

typedef seqan::Align<TSequence,seqan::ArrayGaps> TAlign;

TSequence seq1 = "CDFGAAAHC";

TSequence seq2 = "CDEFGAHC";

TAlign align;

resize(rows(align), 2);

assignSource(row(align,0),seq1);

assignSource(row(align,1),seq2);

double score = globalAlignment(align, seqan::Score<int, seqan::ScoreMatrix<seqan::AminoAcid, seqan::Blosum62_>>());

std::cout << "Score: " << score << ::std::endl;

std::cout << align << ::std::endl;

Thanks for any and all help!

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

--------------070805010907080202050905-- From laeciofreitas@gmail.com Fri Jan 24 16:49:58 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1W6j12-002SLk-OM>; Fri, 24 Jan 2014 16:49:56 +0100 Received: from mail-lb0-f176.google.com ([209.85.217.176]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1W6j12-0049bP-La>; Fri, 24 Jan 2014 16:49:56 +0100 Received: by mail-lb0-f176.google.com with SMTP id w7so2673251lbi.35 for ; Fri, 24 Jan 2014 07:49:55 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:from:date:message-id:subject:to:content-type; bh=aA1jP3ODPqLFFENyxbIO3dAfNnsABSkbywybjnNSaMs=; b=KE1WbCMywpBchITkPidPP9AXPeaqMrPwir5T01JCCSn4wU04zk2V7jlj7U3JWDK2M8 sjWDE/AJlvrkaKaq0dM3FIAW9UrOlj7VJ9dge4mlT/w7lZl+Z1ueW07vcTXB0pH6JxMj OgClY5dNTL2PFCixlao5PweoxLdidd9NFFcqeYtZofCPm0cTDFSGExz66ZAQ2/tYqw2P /0TrisTuyCBl35mX+AmfNOo1WVk7ZuSk5m7VZnX0C+HKFKzYsB40U20ZFABZhR0NotiG DSQkZHPlL7U92yCkucELBabzSKHOSFZ8JEA+NXOiR2pjP44Lx7KRA1oD8y8TnWf5VTrD gY/A== X-Received: by 10.152.20.6 with SMTP id j6mr9353891lae.8.1390578595140; Fri, 24 Jan 2014 07:49:55 -0800 (PST) MIME-Version: 1.0 Received: by 10.114.169.226 with HTTP; Fri, 24 Jan 2014 07:49:35 -0800 (PST) From: =?ISO-8859-1?Q?La=E9cio_Freitas_Chaves?= Date: Fri, 24 Jan 2014 13:49:35 -0200 Message-ID: To: SeqAn Development Content-Type: multipart/alternative; boundary=089e013d203432178304f0b94f4d X-Originating-IP: 209.85.217.176 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1390578596-0000CD40-FB57A75A/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.492916, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Schemes to weight X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 24 Jan 2014 15:49:58 -0000 --089e013d203432178304f0b94f4d Content-Type: text/plain; charset=ISO-8859-1 Hi, Where can I find more detailed information of these weights: http://docs.seqan.de/seqan/dev3/group_AlignmentGraphCombinationTags.html What line and file these weights are implemented? --089e013d203432178304f0b94f4d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hi,

Where can I find more deta= iled information of these weights:

http://docs.seqan.de/seqan/dev3/group_AlignmentGraphCombinationTags.ht= ml

What line and file these=A0weights=A0are implemented?

--089e013d203432178304f0b94f4d--