From gburgess@hawaii.edu Sat Oct 29 03:19:00 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1c0IIW-001nk9-5w>; Sat, 29 Oct 2016 03:19:00 +0200 Received: from mail-qk0-f172.google.com ([209.85.220.172]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:AES128-GCM-SHA256:128) (envelope-from ) id <1c0IIV-001oKG-VM>; Sat, 29 Oct 2016 03:19:00 +0200 Received: by mail-qk0-f172.google.com with SMTP id v138so16260790qka.0 for ; Fri, 28 Oct 2016 18:18:58 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=hawaii-edu.20150623.gappssmtp.com; s=20150623; h=mime-version:from:date:message-id:subject:to; bh=fvgguBRKS8owUSpB8TxdTkiCwL1nVw2w4L4F3ZLfvQw=; b=hfJju0cocD3QtwhJUcyR42vNH7YbV9H9YCU6ew5Ef3pYRBcX4ntZdUSGaiiavzS/SV v2poiopXsH338hp/kummJYotuHCuJDwibmU6XhSpvK9a9IJPzPmtOH425ulasjkGuy8R ZpyacoprsRL8zwcgK/JbEdRpkcRNX939eRZPvD60qXM9HtOYbaWPq08flk9lop9klQd3 QBbsenCmyvEWD6Q/4uSot38+C35/d8G7FJQz+P/PL4azBCRTS8JdDC1Z1cF7gx4013CM k9sMNCnYaAuIqlRdQPc5G32Vi4GL6251XbO89j22BZYDmz5BXScylisv19MaIE1VK55W tg6w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=fvgguBRKS8owUSpB8TxdTkiCwL1nVw2w4L4F3ZLfvQw=; b=IVygYKuFo1Uwz/t1pnqVZ3e38nMhD2mFvIoQJ41xkCahZR8PxB/KiBotFfoQh+XjF+ +ItOrpkzuoFiq6jFfxvru6ioFrOYZczJE4MGgMdejBu7JxMOkOQ4/VxQ4MPgi/QHoGg2 lixY4ZqWCK6TnerhlLisVNe1kzm4S7vrcvJUXpQNXcoYMWCpKGG3ArRyIL3JYGO0AGzR 1BWD7eW0ALmOUR0qQsGHnSwurbWmTEkTfYPblL5wVlbAOrCT7rCjLEqrZeJ+xzKcvQRi FkPxYoHN3a82dc7lMewYk8bkOq1zKK4pzhRAXPx8vvbCfoID9eXy+f0/TTWm/1bQV1B4 Xzug== X-Gm-Message-State: ABUngve9p29+R5dt3cVOmc0MrpnmVHeFpbqtZyeP6S6xllQjslQ3+OR14F1+v8u3hqlrA0KWM+wjVFuLkgObuhKn X-Received: by 10.55.107.6 with SMTP id g6mr8962153qkc.178.1477703937529; Fri, 28 Oct 2016 18:18:57 -0700 (PDT) MIME-Version: 1.0 Received: by 10.12.170.81 with HTTP; Fri, 28 Oct 2016 18:18:57 -0700 (PDT) From: Gregory Burgess Date: Fri, 28 Oct 2016 15:18:57 -1000 Message-ID: To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=001a114875fc4810ba053ff6c2c9 X-Originating-IP: 209.85.220.172 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1477703940-000004B9-71FAE440/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.190557, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.2 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, HTML_MESSAGE,RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H2,RCVD_IN_SORBS_SPAM,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.1 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Realigning over Amino Acids 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: Sat, 29 Oct 2016 01:19:00 -0000 --001a114875fc4810ba053ff6c2c9 Content-Type: text/plain; charset=UTF-8 Hi, I'm using seqan 1.4.1. I have a fasta file of aligned (gap characters included) amino acid sequences. I would like to simply read in this file and use seqan's realign function over these sequences. I see that realign() requires a Fragment Store, but I'm not sure how to generate the appropriate data structures from already-aligned amino acid sequences. Can someone provide a general outline of this (or another approach)? Thanks, Greg --001a114875fc4810ba053ff6c2c9 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi,

I'm using seqan 1.4.1.=C2=A0 I have a fasta file o= f aligned (gap characters included) amino acid sequences.=C2=A0 I would lik= e to simply read in this file and use seqan's realign function over the= se sequences.=C2=A0

I see that realign() requires a Fragment Store, but= I'm not sure how to generate the appropriate data structures from alre= ady-aligned amino acid sequences.=C2=A0 Can someone provide a general outli= ne of this (or another approach)?

Thanks,
Greg
--001a114875fc4810ba053ff6c2c9-- From hannes.hauswedell@fu-berlin.de Sat Oct 29 16:03:01 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1c0UDt-002X7Q-8u>; Sat, 29 Oct 2016 16:03:01 +0200 Received: from einhorn.in-berlin.de ([192.109.42.8]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1c0UDt-003j0i-4g>; Sat, 29 Oct 2016 16:03:01 +0200 X-Envelope-From: hannes.hauswedell@fu-berlin.de X-Envelope-To: Received: from fbsdmain.soldiner.lan (soulrebel.in-vpn.de [217.197.85.230]) (authenticated bits=0) by einhorn.in-berlin.de (8.14.4/8.14.4/Debian-8+deb8u1) with ESMTP id u9TE2x0r008057 (version=TLSv1/SSLv3 cipher=ECDHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sat, 29 Oct 2016 16:02:59 +0200 To: "seqan-dev@lists.fu-berlin.de" References: From: Hannes Hauswedell Message-ID: <658225fe-c121-8c13-4159-13e3c396a898@fu-berlin.de> Date: Sat, 29 Oct 2016 16:02:59 +0200 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Originating-IP: 192.109.42.8 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1477749781-000004B9-487965BE/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.1 required=5.0 tests=RCVD_IN_DNSWL_LOW, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_NEUTRAL,T_FILL_THIS_FORM_SHORT, URIBL_BLOCKED X-Spam-Checker-Version: SpamAssassin 3.4.1 on Tokelau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Realigning over Amino Acids 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: Sat, 29 Oct 2016 14:03:01 -0000 On 29.10.2016 03:18, Gregory Burgess wrote: > Hi, > > I'm using seqan 1.4.1. I have a fasta file of aligned (gap characters > included) amino acid sequences. I would like to simply read in this > file and use seqan's realign function over these sequences. > > I see that realign() requires a Fragment Store, but I'm not sure how to > generate the appropriate data structures from already-aligned amino acid > sequences. Can someone provide a general outline of this (or another > approach)? > > Thanks, > Greg Dear Greg, SeqAn-1.4.1 is not developed anymore (since quite some time now). Please reproduce your problem with a current release and open an issue on github.com/seqan/seqan if the problem persists. If you don't want to use the fragment store I would recommend reading the alignment into an AlignmentGraph and then call globalAlignment() on that, possibly with a small band if performance is important. Best regards, Hannes -- Hannes Hauswedell PhD student Max Planck Institute for Molecular Genetics / Freie Universität Berlin address Institut für Informatik Takustraße 9 Room 019 14195 Berlin telephone +49 (0)30 838-75241 fax +49 (0)30 838-75218 e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]