From Sabrina.Krakau@fu-berlin.de Wed Jul 03 11:37:09 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) with esmtp (envelope-from ) id <1UuJUp-0043n0-I1>; Wed, 03 Jul 2013 11:37:07 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) with esmtp (envelope-from ) id <1UuJUp-0023Lm-Fi>; Wed, 03 Jul 2013 11:37:07 +0200 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) with esmtp (envelope-from ) id <1UuJUp-002udU-6R>; Wed, 03 Jul 2013 11:37:07 +0200 Received: from EX03A.campus.fu-berlin.de ([130.133.170.134]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0123.003; Wed, 3 Jul 2013 11:34:27 +0200 From: "Krakau, Sabrina" Thread-Topic: SeqAn - BioStore Workshop 2013, Berlin, September 17th - 19th Thread-Index: Ac530IHPv7HRBBlCTr6kRCJFPyIUGg== Message-ID: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: yes X-MS-TNEF-Correlator: Content-Type: multipart/mixed; boundary="_004_CBC5629F5E78A84A853AD8A3D5AF81BF51CEC9D2ex03acampusfube_" MIME-Version: 1.0 Date: Wed, 03 Jul 2013 11:34:26 +0200 X-Original-Date: Wed, 3 Jul 2013 09:34:26 +0000 X-Originating-IP: 130.133.170.203 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1372844227-0000097E-D9C52BF7/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000002, version=1.2.3 X-Spam-Flag: NO X-Spam-Status: No, score=-48.8 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE, MISSING_HEADERS X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Cc: AG ABI ABI , SeqAn Development , "seqan-interests@lists.fu-berlin.de" Subject: [Seqan-dev] SeqAn - BioStore Workshop 2013, Berlin, September 17th - 19th X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 03 Jul 2013 09:37:09 -0000 --_004_CBC5629F5E78A84A853AD8A3D5AF81BF51CEC9D2ex03acampusfube_ Content-Type: multipart/alternative; boundary="_000_CBC5629F5E78A84A853AD8A3D5AF81BF51CEC9D2ex03acampusfube_" --_000_CBC5629F5E78A84A853AD8A3D5AF81BF51CEC9D2ex03acampusfube_ Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: quoted-printable Dear SeqAn Users and Developers, We would like to invite you to the annual SeqAn - BioStore Workshop 2013. Date September 17th - 19th (Tuesday - Thursday) Location Freie Universit=E4t Berlin Institute of Computer Science Takustr. 9, 14195 Berlin Target Group The workshop is suitable for both beginners and advanced SeqAn users and de= velopers. Contents This year's schedule will include: * Introduction to SeqAn, new features and highlights * SeqAn tutorials for beginners and advanced programmers * Presentation of SeqAn apps, as well as of external apps using SeqAn * Workflows in KNIME with SeqAn * Talks about external projects using SeqAn As a highlight of the workshop, we will organize a dinner on board of a cru= ise ship on the Spree river. Detailed information about the schedule will follow soon. If you have any questions until then, don't hesitate to send an email to sa= brina.krakau@fu-berlin.de. Please forward this invitation to your colleagues who might be interested. For general information you can visit the BioStore project website: www.seqan-biostore.de and the SeqAn website: www.seqan.de We are looking forward to see you all in September. The SeqAn team -- Sabrina Krakau [Logo] Freie Universit=E4t Berlin Institute of Computer Science Algorithmic Bioinformatics - Project BioStore Takustr. 9, 14195 Berlin Telefon: +49 (0)30 838 75228 --_000_CBC5629F5E78A84A853AD8A3D5AF81BF51CEC9D2ex03acampusfube_ Content-Type: text/html; charset="iso-8859-2" Content-Transfer-Encoding: quoted-printable Dear SeqAn Users and Developers,

We would like to invite you to the annual SeqAn - BioStore Workshop 2013.
Date
September 17th - 19th
(Tuesday - Thursday)

Location
Freie Universit=E4t Berlin
Institute of Computer Science
Takustr. 9, 14195 Berlin

Target Group
The workshop is suitable for both beginners and advanced SeqAn users and de= velopers.

Contents
This year's schedule will include:
  • Introduction to SeqAn, new features and highlights
  • SeqAn tutorials for beginners and advanced programmers
  • Presentation of SeqAn apps, as well as of external apps using SeqA= n
  • Workflows in KNIME with SeqAn
  • Talks about external projects using SeqAn

As a highlight of the workshop, we will organize a dinner on board of a cru= ise ship on the Spree river.

Detailed information about the schedule will follow soon.
If you have any questions until then, don't hesitate to send an email to sabrina.krakau@fu-berlin.de.
Please forward this invitation to your colleagues who might be interested.<= br>
For general information you can visit the BioStore project website:
    www.seqan-biost= ore.de

and the SeqAn website:
    www.seqan.de

We are looking forward to see you all in September.
The SeqAn team

--

Sabrina Krakau

3D"Logo"

Freie Universit=E4t Berlin
Institute of Computer Science
Algorithmic Bioinformatics - Project BioStore

Takustr. 9, 14195 Berlin
Telefon: +49 (0)30 838 75228

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Thu, 11 Jul 2013 10:01:43 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UxBos-001hzy-Sm>; Thu, 11 Jul 2013 10:01:42 +0200 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UxBos-001JDN-FF>; Thu, 11 Jul 2013 10:01:42 +0200 Received: from EX02B.campus.fu-berlin.de ([130.133.170.133]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0123.003; Thu, 11 Jul 2013 10:01:41 +0200 From: "Holtgrewe, Manuel" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: [ANN] New SeqAn Version 1.4.1 Released Thread-Index: Ac5+DOBjHZtSFcTSTy+LOxV5lRwa0A== Message-ID: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Date: Thu, 11 Jul 2013 10:01:40 +0200 X-Original-Date: Thu, 11 Jul 2013 08:01:40 +0000 X-Originating-IP: 130.133.170.202 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1373529702-0000097E-2DE82BE1/0-0/0-0 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 X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] [ANN] New SeqAn Version 1.4.1 Released X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 11 Jul 2013 08:01:44 -0000 Hi everyone,=0A= =0A= the SeqAn team is happy to announce the 1.4.1 release of the SeqAn apps and= libraries. This update includes some new features and bug fixes from the 1= .4.0 release but should be compatible to 1.4.0 otherwise.=0A= =0A= You can download the release packages at http://packages.seqan.de.=0A= =0A= The highlights are=0A= =0A= * many new demos and improved API documentation throughout the library and= for central classes, and=0A= * new file format support and tutorials for this: VCF, BED, GFF.=0A= =0A= We recommend everyone to upgrade to the new version.=0A= =0A= You can find a more extensive list of changes at [2].=0A= =0A= Enjoy!=0A= The SeqAn Team=0A= =0A= [1] http://packages.seqan.de=0A= [2] http://trac.seqan.de/wiki/ChangeLog#Release1.4.1= From gorkeralp@gmail.com Mon Jul 15 16:11:50 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UyjVF-003oyB-31>; Mon, 15 Jul 2013 16:11:49 +0200 Received: from mail-ve0-f169.google.com ([209.85.128.169]) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UyjVE-000Isc-TY>; Mon, 15 Jul 2013 16:11:49 +0200 Received: by mail-ve0-f169.google.com with SMTP id m1so10078208ves.0 for ; Mon, 15 Jul 2013 07:11:46 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:sender:from:date:x-google-sender-auth:message-id :subject:to:content-type; bh=Uh1WRiFRUhVCjY4xy/h+zYI1q1uUa2YkltIwVquOG3c=; b=PkPnd6wlnYzTyYYD6m8STGb43AHVjI6S4TCSGHsPQ8/g/iL87SlycwpSh+/FMcS45I fl3RJN7kiYELf/fjhNHC35VoEYcd/g/llSej0Bct4ZvBczBdmZ/RjNqf6/vLvMwvjHvP 6ciiBtIZrBoi/4PUmhQB/BPRbVUgrpgOD5+1jLwytXtw/tZ/JZ7X7SnSm8eEeZaAvaw/ Yu4nA+GcXFiDpNsrhzaIIRYwbiF8CmmDjrKGYyHcb/O/HHw+nt8jOBcdaRsHCUl8+yf9 umzaswe4tfsnPb6JgogzOwiyvPA/9KKFi8eEKIxj/OhJfN7oG16NFpu8nRUFZMLSiSG8 DW+w== X-Received: by 10.58.76.130 with SMTP id k2mr7635999vew.24.1373897506801; Mon, 15 Jul 2013 07:11:46 -0700 (PDT) MIME-Version: 1.0 Sender: gorkeralp@gmail.com Received: by 10.58.196.210 with HTTP; Mon, 15 Jul 2013 07:11:16 -0700 (PDT) From: F M Date: Mon, 15 Jul 2013 17:11:16 +0300 X-Google-Sender-Auth: -6c-3GSjbrkYB9hM3FXG1l7IC7c Message-ID: To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=047d7b3a86f6d9d00704e18d7011 X-Originating-IP: 209.85.128.169 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1373897509-0000097E-DF5BFF8D/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.056684, 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 Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Appr. BNDM algorithm X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 15 Jul 2013 14:11:50 -0000 --047d7b3a86f6d9d00704e18d7011 Content-Type: text/plain; charset=ISO-8859-1 Hello, as a phd student curious to learn string matching algorithm implementations, I have been checking seqan tutorials since this morning :) my question is how is Approximate Backward Nondeterministic Dawg Matching implemented? How does scoring work? What kind of metric is this? Is there a research paper that explains the inner details? Thank you. Best Regards, Alp http://docs.seqan.de/seqan/dev/SPEC_Abndm_Algo.html --047d7b3a86f6d9d00704e18d7011 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello, as a phd student curious to learn string matchin= g algorithm implementations, I have been checking seqan tutorials since thi= s morning :)
my question is how is Approximate Backward Nondeterministic Dawg Matchin= g implemented? How does scoring work? What kind of metric is this? Is there= a research paper that explains the inner details? Thank you.
= Best Regards,
Alp

http://docs.se= qan.de/seqan/dev/SPEC_Abndm_Algo.html
--047d7b3a86f6d9d00704e18d7011-- From manuel.holtgrewe@fu-berlin.de Mon Jul 15 16:45:49 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Uyk28-003tmV-NT>; Mon, 15 Jul 2013 16:45:48 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Uyk28-002Bax-Kr>; Mon, 15 Jul 2013 16:45:48 +0200 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Uyk28-002cF4-9k>; Mon, 15 Jul 2013 16:45:48 +0200 Received: from EX02B.campus.fu-berlin.de ([130.133.170.133]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.03.0123.003; Mon, 15 Jul 2013 16:45:47 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] Appr. BNDM algorithm Thread-Index: AQHOgWVE7mFY0vXhAEKDVJbmGHyt/5ll0L5L 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_FCCAB9D80C3DAB47B5601C5B0E62872B4578BB5Fex02bcampusfube_" MIME-Version: 1.0 Date: Mon, 15 Jul 2013 16:45:45 +0200 X-Original-Date: Mon, 15 Jul 2013 14:45:45 +0000 X-Originating-IP: 130.133.170.201 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1373899548-0000097E-05951B2F/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000092, 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 Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Appr. BNDM algorithm X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 15 Jul 2013 14:45:50 -0000 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B4578BB5Fex02bcampusfube_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Alp, the score is the negative edit distance (i.e. 3 edit distance errors -> sco= re of -3). The algorithm was not invented by any SeqAn people but rather is described = in Navarro's book: Navarro, Gonzalo, and Matthieu Raffinot. Flexible pattern matching in strin= gs: practical on-line search algorithms for texts and biological sequences.= Cambridge University Press, 2002. Cheers, Manuel ________________________________ From: F M [flying.madden@gmail.com] Sent: Monday, July 15, 2013 4:11 PM To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] Appr. BNDM algorithm Hello, as a phd student curious to learn string matching algorithm implemen= tations, I have been checking seqan tutorials since this morning :) my question is how is Approximate Backward Nondeterministic Dawg Matching i= mplemented? How does scoring work? What kind of metric is this? Is there a = research paper that explains the inner details? Thank you. Best Regards, Alp http://docs.seqan.de/seqan/dev/SPEC_Abndm_Algo.html --_000_FCCAB9D80C3DAB47B5601C5B0E62872B4578BB5Fex02bcampusfube_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi Alp,

the score is the negative edit distance (i.e. 3 edit distance errors -= > score of -3).

The algorithm was not invented by any SeqAn people but rather is descr= ibed in Navarro's book:

Navarro, Gonzalo= , and Matthieu Raffinot. Flexible pattern matching in strings: practical on-line search algorithms for texts= and biological sequences. Cambridge University Press, 2002.

Cheers,
Manuel

From: F M [flying.madden@gmail.com]
Sent: Monday, July 15, 2013 4:11 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Appr. BNDM algorithm

Hello, as a phd student curious to learn string matching algorithm imp= lementations, I have been checking seqan tutorials since this morning :)
my question is how is Approximate Backward Nondeterministic Dawg Match= ing implemented? How does scoring work? What kind of metric is this? Is there a research paper that explains the i= nner details? Thank you.
Best Regar= ds,
Alp=

http://docs.seqan.de/seqan/dev/SPEC_Abndm_Algo.html