From wengl@uci.edu Thu Jun 16 01:24:08 2011 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 <1QWzRO-0001FL-QO>; Thu, 16 Jun 2011 01:24:06 +0200 Received: from smtp2.es.uci.edu ([128.200.80.32]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QWzRO-0002Ap-C6>; Thu, 16 Jun 2011 01:24:06 +0200 Received: from [128.195.53.171] (dhcp-053171.ics.uci.edu [128.195.53.171]) (authenticated bits=0) by smtp2.es.uci.edu (8.13.8/8.13.8) with ESMTP id p5FNO2cx022876 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Wed, 15 Jun 2011 16:24:03 -0700 X-UCInetID: wengl Message-ID: <4DF940F3.7040708@uci.edu> Date: Wed, 15 Jun 2011 16:32:03 -0700 From: Lingjie Weng User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.9.2.14) Gecko/20110223 Thunderbird/3.1.8 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary="------------030106070804070700060302" X-Originating-IP: 128.200.80.32 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1308180246-00005A17-F7AEABC0/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.145900, 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=0.9 required=5.0 tests=HTML_40_50,HTML_MESSAGE, RATWARE_GECKO_BUILD Subject: [Seqan-dev] Combine bit-parallel algorithm with Ukkonens trick for globalAlignment 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: Wed, 15 Jun 2011 23:24:08 -0000 This is a multi-part message in MIME format. --------------030106070804070700060302 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear Seqan team, I am interested in our Seqan C++ library, it is really helpful. I am curious whether "MyersBitVector " algorithm in globalalignment has already combined with Ukkonens algorithm. I found you have MyersUkkonen in pattern matching, I am wondering if you have such implementation which could be used for sequence alignment, mainly for computing the levenshtein edit distance. Thank you for your patience. Thanks, Lingjie PhD student University of California, Irvine --------------030106070804070700060302 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Seqan team,

I am interested in our Seqan C++ library, it is really helpful. I am curious whether "MyersBitVector " algorithm in globalalignment has already combined with Ukkonens algorithm.

I found you have MyersUkkonen in pattern matching, I am wondering if you have such implementation which could be used for sequence alignment, mainly for computing the levenshtein edit distance. Thank you for your patience.

Thanks,
Lingjie

PhD student
University of California, Irvine


--------------030106070804070700060302-- From weese@campus.fu-berlin.de Mon Jun 20 22:37:19 2011 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 <1QYlDh-0004zu-W9>; Mon, 20 Jun 2011 22:37:18 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QYlDh-0006aq-Tp>; Mon, 20 Jun 2011 22:37:17 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1QYlDh-0000cA-OI>; Mon, 20 Jun 2011 22:37:17 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 20 Jun 2011 22:37:17 +0200 From: "Weese, David" To: SeqAn Development Date: Mon, 20 Jun 2011 22:37:16 +0200 Thread-Topic: [Seqan-dev] Combine bit-parallel algorithm with Ukkonens trick for globalAlignment Thread-Index: AcwvidgBUyVxec6BSUmeQITxXeM08A== Message-ID: <70C6CB63-B71E-43EA-B7FB-6AD02F3389AA@fu-berlin.de> References: <4DF940F3.7040708@uci.edu> In-Reply-To: <4DF940F3.7040708@uci.edu> Accept-Language: de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE Content-Type: multipart/alternative; boundary="_000_70C6CB63B71E43EAB7FB6AD02F3389AAfuberlinde_" MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1308602237-00005A17-2BA9A61F/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.078761, 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-Spam-Status: No, score=-2.7 required=5.0 tests=ALL_TRUSTED,HTML_40_50, HTML_MESSAGE Subject: Re: [Seqan-dev] Combine bit-parallel algorithm with Ukkonens trick for globalAlignment 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, 20 Jun 2011 20:37:19 -0000 --_000_70C6CB63B71E43EAB7FB6AD02F3389AAfuberlinde_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Lingjie, yes, the implementation of Myers' bitvector algorithm for large patterns in= corporates the Ukkonen algorithm to save computation time. Cheers, David Am 16.06.2011 um 01:32 schrieb Lingjie Weng: Dear Seqan team, I am interested in our Seqan C++ library, it is really helpful. I am curiou= s whether "MyersBitVector " algorithm in globalalignment has already combin= ed with Ukkonens algorithm. I found you have MyersUkkonen in pattern matching, I am wondering if you ha= ve such implementation which could be used for sequence alignment, mainly f= or computing the levenshtein edit distance. Thank you for your patience. Thanks, Lingjie PhD student University of California, Irvine _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev --_000_70C6CB63B71E43EAB7FB6AD02F3389AAfuberlinde_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Lingjie,

<= /div>
yes, the implementation of Myers' bitvector algorithm for large p= atterns incorporates the Ukkonen algorithm to save computation time.
<= div>
Cheers,
David


Am 16.06.2011 um 01:32 schrieb Lingjie Weng:

Dear Seqan team,

I am interested in our Seqan C++ library, it is really helpful. I am curious whether "MyersBitVector " algorithm in globalalignment has already combined with Ukkonens algorithm.

I found you have MyersUkkonen in pattern matching, I am wondering if you have such implementation which could be used for sequence alignment, mainly for computing the levenshtein edit distance. Thank you for your patience.

Thanks,
Lingjie

PhD student
University of California, Irvine


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

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