From manuel.holtgrewe@fu-berlin.de Mon Aug 02 13:46:16 2010 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1OftTC-0006BX-Kv>; Mon, 02 Aug 2010 13:46:14 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1OftTC-00056C-J5>; Mon, 02 Aug 2010 13:46:14 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1OftTC-0001SZ-GX>; Mon, 02 Aug 2010 13:46:14 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 2 Aug 2010 13:45:49 +0200 From: "Holtgrewe, Manuel" To: Sven Nahnsen Date: Mon, 2 Aug 2010 13:46:13 +0200 Thread-Topic: seqan Thread-Index: AcsyOECHECSn9llMTI+V9q6yVKwcQQ== Message-ID: <87E39A2E-1AFE-4B8B-96EA-BC05BE587C8D@fu-berlin.de> References: <4C56916F.6090607@informatik.uni-tuebingen.de> <4C56A0AE.3060000@mi.fu-berlin.de> <7D47109C-721A-45D6-AA80-B00FA6864129@fu-berlin.de> <4C56A886.40601@informatik.uni-tuebingen.de> In-Reply-To: <4C56A886.40601@informatik.uni-tuebingen.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1280749574-000069FD-A8FDC5D3/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000158, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Cc: "seqan-dev@lists.fu-berlin.de" Subject: Re: [Seqan-dev] seqan X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 02 Aug 2010 11:46:17 -0000 Hi Sven, have a look at the new "init_score.cpp" demo. I just committed it into trun= k. To build it, update your trunk checkout, go to your cmake directory, execut= e cmake again. Then, you can execute "make init_score", build it and execut= e it via "./demos/init_score". You can find the source code here: https://trac.mi.fu-berlin.de/seqan/browser/trunk/seqan/projects/library/dem= os/init_score.cpp The demo shows how to initialize the matrix using one of the built-in stati= c matrices, how to define your own static matrix and how to initialize it b= y setting the values manually. HTH *m Am 02.08.2010 um 13:14 schrieb Sven Nahnsen: > Hi Manuel, >=20 > I work with OpenMS and I use some SEQAN funtionality to score pairwise=20 > sequence alignments of peptides. > This works nicely while using your predefined matrices, such as Blosum62= =20 > or the PAM matrices. >=20 > I use the following code: > ///////////////////////////// > ::seqan::Align align; > ::seqan::resize(rows(align), 2); > ::seqan::assignSource(row(align, 0), seq1); > ::seqan::assignSource(row(align, 1), seq2); > ::seqan::Score > pam(PAM, -opening_penalty,=20 > -extension_penalty); > c =3D (DoubleReal)globalAlignment(align, pam,::seqan::NeedlemanWunsch()); > /////////////////////////// >=20 > However I would like to use a slightly modified PAM matrix (PAM30MS),=20 > that is specifically designed for my purposes. > From your documentation I so far couldn't figure out how to initialize=20 > the entries of a new (24x24) matrix. >=20 > Thanks for your help! >=20 > Best, >=20 > Sven >=20 >=20 >=20 >=20 > On 02.08.2010 12:44, Holtgrewe, Manuel wrote: >> Hi Sven, >>=20 >> Ich beantworte deine Frage gerne. Stell die ganze Frage und was du genau= machen willst doch mal an die SeqAn Mailing Liste >>=20 >> https://lists.fu-berlin.de/listinfo/seqan-dev >>=20 >> Dann haben alle die im Archiv nachsehen was davon ;) >>=20 >> *m >>=20 >> Am 02.08.2010 um 12:40 schrieb Chris Bielow: >>=20 >>=20 >=20 From manuel.holtgrewe@fu-berlin.de Mon Aug 02 13:59:18 2010 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Oftfo-0006d4-Mo>; Mon, 02 Aug 2010 13:59:16 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1Oftfo-0007lW-Kq>; Mon, 02 Aug 2010 13:59:16 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1Oftfo-0002Vq-IL>; Mon, 02 Aug 2010 13:59:16 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 2 Aug 2010 13:58:51 +0200 From: "Holtgrewe, Manuel" To: "Holtgrewe, Manuel" Date: Mon, 2 Aug 2010 13:59:15 +0200 Thread-Topic: seqan Thread-Index: AcsyOhJKDHymFw4AQtyGhZ8P+K62IA== Message-ID: <30B6B26C-B699-4F51-BB16-BC664F5EFE1D@fu-berlin.de> References: <4C56916F.6090607@informatik.uni-tuebingen.de> <4C56A0AE.3060000@mi.fu-berlin.de> <7D47109C-721A-45D6-AA80-B00FA6864129@fu-berlin.de> <4C56A886.40601@informatik.uni-tuebingen.de> <87E39A2E-1AFE-4B8B-96EA-BC05BE587C8D@fu-berlin.de> In-Reply-To: <87E39A2E-1AFE-4B8B-96EA-BC05BE587C8D@fu-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1280750356-000069FD-BFE9A1C6/3179398549-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000041, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=ALL_TRUSTED,FU_XPURGATE_SUSP Cc: "seqan-dev@lists.fu-berlin.de" , Sven Nahnsen Subject: Re: [Seqan-dev] seqan X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 02 Aug 2010 11:59:18 -0000 Whoops, I guess the HTTPS site is password protected http://trac.mi.fu-berlin.de/seqan/browser/trunk/seqan/projects/library/demo= s/init_score.cpp Access should be public there. *m Am 02.08.2010 um 13:46 schrieb Holtgrewe, Manuel: > Hi Sven, >=20 > have a look at the new "init_score.cpp" demo. I just committed it into tr= unk. >=20 > To build it, update your trunk checkout, go to your cmake directory, exec= ute cmake again. Then, you can execute "make init_score", build it and exec= ute it via "./demos/init_score". >=20 > You can find the source code here: >=20 > https://trac.mi.fu-berlin.de/seqan/browser/trunk/seqan/projects/library/d= emos/init_score.cpp >=20 > The demo shows how to initialize the matrix using one of the built-in sta= tic matrices, how to define your own static matrix and how to initialize it= by setting the values manually. >=20 > HTH > *m >=20 > Am 02.08.2010 um 13:14 schrieb Sven Nahnsen: >=20 >> Hi Manuel, >>=20 >> I work with OpenMS and I use some SEQAN funtionality to score pairwise=20 >> sequence alignments of peptides. >> This works nicely while using your predefined matrices, such as Blosum62= =20 >> or the PAM matrices. >>=20 >> I use the following code: >> ///////////////////////////// >> ::seqan::Align align; >> ::seqan::resize(rows(align), 2); >> ::seqan::assignSource(row(align, 0), seq1); >> ::seqan::assignSource(row(align, 1), seq2); >> ::seqan::Score > pam(PAM, -opening_penalty,=20 >> -extension_penalty); >> c =3D (DoubleReal)globalAlignment(align, pam,::seqan::NeedlemanWunsch())= ; >> /////////////////////////// >>=20 >> However I would like to use a slightly modified PAM matrix (PAM30MS),=20 >> that is specifically designed for my purposes. >> From your documentation I so far couldn't figure out how to initialize=20 >> the entries of a new (24x24) matrix. >>=20 >> Thanks for your help! >>=20 >> Best, >>=20 >> Sven >>=20 >>=20 >>=20 >>=20 >> On 02.08.2010 12:44, Holtgrewe, Manuel wrote: >>> Hi Sven, >>>=20 >>> Ich beantworte deine Frage gerne. Stell die ganze Frage und was du gena= u machen willst doch mal an die SeqAn Mailing Liste >>>=20 >>> https://lists.fu-berlin.de/listinfo/seqan-dev >>>=20 >>> Dann haben alle die im Archiv nachsehen was davon ;) >>>=20 >>> *m >>>=20 >>> Am 02.08.2010 um 12:40 schrieb Chris Bielow: >>>=20 >>>=20 >>=20 >=20 From nahnsen@informatik.uni-tuebingen.de Mon Aug 02 13:14:18 2010 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1OfsyG-0005A9-7x>; Mon, 02 Aug 2010 13:14:16 +0200 Received: from mx2.informatik.uni-tuebingen.de ([134.2.12.9]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with smtp (envelope-from ) id <1OfsyG-00008K-45>; Mon, 02 Aug 2010 13:14:16 +0200 Received: from localhost (localhost [127.0.0.1]) by mx2.informatik.uni-tuebingen.de (Postfix) with ESMTP id 4FCC03471; Mon, 2 Aug 2010 13:14:15 +0200 (MEST) Received: from mx2.informatik.uni-tuebingen.de ([127.0.0.1]) by localhost (mx2.informatik.uni-tuebingen.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id iIAREf8-1vcB; Mon, 2 Aug 2010 13:14:15 +0200 (MEST) Received: from imap.informatik.uni-tuebingen.de (bluff [134.2.9.80]) by mx2.informatik.uni-tuebingen.de (Postfix) with ESMTP id F01D13442; Mon, 2 Aug 2010 13:14:14 +0200 (MEST) Received: from [134.2.9.178] (sutent [134.2.9.178]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by imap.informatik.uni-tuebingen.de (Postfix) with ESMTP id DD9155C60; Mon, 2 Aug 2010 13:14:14 +0200 (MEST) Message-ID: <4C56A886.40601@informatik.uni-tuebingen.de> Date: Mon, 02 Aug 2010 13:14:14 +0200 From: Sven Nahnsen User-Agent: Mozilla/5.0 (Windows; U; Windows NT 6.1; en-US; rv:1.9.1.11) Gecko/20100711 Thunderbird/3.0.6 MIME-Version: 1.0 To: "Holtgrewe, Manuel" , seqan-dev@lists.fu-berlin.de References: <4C56916F.6090607@informatik.uni-tuebingen.de> <4C56A0AE.3060000@mi.fu-berlin.de> <7D47109C-721A-45D6-AA80-B00FA6864129@fu-berlin.de> In-Reply-To: <7D47109C-721A-45D6-AA80-B00FA6864129@fu-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 134.2.12.9 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1280747656-000069FD-0FBB3B92/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.001282, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD X-Mailman-Approved-At: Thu, 05 Aug 2010 08:30:10 +0200 Subject: Re: [Seqan-dev] seqan X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 02 Aug 2010 11:14:18 -0000 Hi Manuel, I work with OpenMS and I use some SEQAN funtionality to score pairwise sequence alignments of peptides. This works nicely while using your predefined matrices, such as Blosum62 or the PAM matrices. I use the following code: ///////////////////////////// ::seqan::Align align; ::seqan::resize(rows(align), 2); ::seqan::assignSource(row(align, 0), seq1); ::seqan::assignSource(row(align, 1), seq2); ::seqan::Score > pam(PAM, -opening_penalty, -extension_penalty); c = (DoubleReal)globalAlignment(align, pam,::seqan::NeedlemanWunsch()); /////////////////////////// However I would like to use a slightly modified PAM matrix (PAM30MS), that is specifically designed for my purposes. From your documentation I so far couldn't figure out how to initialize the entries of a new (24x24) matrix. Thanks for your help! Best, Sven On 02.08.2010 12:44, Holtgrewe, Manuel wrote: > Hi Sven, > > Ich beantworte deine Frage gerne. Stell die ganze Frage und was du genau machen willst doch mal an die SeqAn Mailing Liste > > https://lists.fu-berlin.de/listinfo/seqan-dev > > Dann haben alle die im Archiv nachsehen was davon ;) > > *m > > Am 02.08.2010 um 12:40 schrieb Chris Bielow: > > From jer15@hermes.cam.ac.uk Thu Aug 26 16:28:54 2010 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1OodRl-000571-92>; Thu, 26 Aug 2010 16:28:53 +0200 Received: from ppsw-30.csi.cam.ac.uk ([131.111.8.130]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1OodRl-0000OI-5p>; Thu, 26 Aug 2010 16:28:53 +0200 X-Cam-AntiVirus: no malware found X-Cam-SpamDetails: not scanned X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from wifi-host-39.mrc-bsu.cam.ac.uk ([193.60.87.39]:38517) by ppsw-30.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.156]:587) with esmtpsa (PLAIN:jer15) (TLSv1:DHE-RSA-AES256-SHA:256) id 1OodRk-0001fP-fY (Exim 4.72) for seqan-dev@lists.fu-berlin.de (return-path ); Thu, 26 Aug 2010 15:28:52 +0100 Message-ID: <4C767A24.6080608@mail.cryst.bbk.ac.uk> Date: Thu, 26 Aug 2010 15:28:52 +0100 From: John Reid User-Agent: Thunderbird 2.0.0.24 (X11/20100411) MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Sender: "J.E. Reid" X-Originating-IP: 131.111.8.130 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1282832933-00000C0F-7B3C7332/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.413800, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.0 required=5.0 tests=none Subject: [Seqan-dev] Which versions of gcc is seqan compatible with? X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 26 Aug 2010 14:28:54 -0000 Hi, Does anyone know which versions of gcc 4 seqan is compatible with? Every new version of gcc seems to adhere to the C++ standard more closely. I cannot compile the latest svn version of seqan with gcc 4.4.1. Thanks, John. From jer15@hermes.cam.ac.uk Tue Aug 31 14:24:07 2010 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1OqPsk-0003Wh-DD>; Tue, 31 Aug 2010 14:24:06 +0200 Received: from ppsw-30.csi.cam.ac.uk ([131.111.8.130]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1OqPsk-0004Zj-AB>; Tue, 31 Aug 2010 14:24:06 +0200 X-Cam-AntiVirus: no malware found X-Cam-SpamDetails: not scanned X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from wifi-host-39.mrc-bsu.cam.ac.uk ([193.60.87.39]:34232) by ppsw-30.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.156]:587) with esmtpsa (PLAIN:jer15) (TLSv1:DHE-RSA-AES256-SHA:256) id 1OqPsk-0000XS-ci (Exim 4.72) for seqan-dev@lists.fu-berlin.de (return-path ); Tue, 31 Aug 2010 13:24:06 +0100 Message-ID: <4C7CF465.3070501@mail.cryst.bbk.ac.uk> Date: Tue, 31 Aug 2010 13:24:05 +0100 From: John Reid User-Agent: Thunderbird 2.0.0.24 (X11/20100411) MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Sender: "J.E. Reid" X-Originating-IP: 131.111.8.130 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1283257446-00000C0F-10205105/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.152699, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.2 required=5.0 tests=HTML_60_70,HTML_MESSAGE, MIME_HTML_ONLY Subject: [Seqan-dev] Suffix tree incorrect behaviour bug in seqan 1.2 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 31 Aug 2010 12:24:07 -0000 Hi,

Ticket 292 describes a case where a suffix tree in release 1.2 of seqan does not behave as expected. Does anyone know if this has been fixed in a later version of seqan in svn? A bug (# 93) with similar symptoms was fixed in revision 4875. Was revision 4875 made before or after release 1.2?

http://trac.mi.fu-berlin.de/seqan/ticket/292
http://trac.mi.fu-berlin.de/seqan/ticket/93

Thanks,
John.