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[128.101.189.185]) by smtp.gmail.com with ESMTPSA id i12-v6sm1284150iom.61.2018.11.20.12.59.45 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Tue, 20 Nov 2018 12:59:45 -0800 (PST) To: seqan-dev@lists.fu-berlin.de From: Lee S Parsons Message-ID: <2a04c653-3839-1bde-e0be-735324ff26a6@umn.edu> Date: Tue, 20 Nov 2018 14:59:45 -0600 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:60.0) Gecko/20100101 Thunderbird/60.2.1 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="------------D8F677A1C7B430015628D563" Content-Language: en-US X-Originating-IP: 134.84.196.207 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1542747590-000004BE-F4EC4263/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000006, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-2.5 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,HTML_MESSAGE,RCVD_IN_DNSWL_MED,SPF_PASS, URIBL_BLOCKED X-Spam-Checker-Version: SpamAssassin 3.4.2 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] SeqAn for proteomics searches in KNIME? X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.29 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 20 Nov 2018 20:59:51 -0000 This is a multi-part message in MIME format. --------------D8F677A1C7B430015628D563 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Hello I would like to use SeqAn to align peptide sequences to protein (FASTA) databases.  Is there a way to do this? I work with a lot of proteomics data in KNIME, and the OpenMS group suggested I look into SeqAn for what I'm trying to do next.  While you probably know that the OpenMS project already has several spectral matching search algorithms built in to it, the project only has one de novo algorithm (compnovo).  While compnovo is a great tool, by virtue of being a de novo algorithm it does not do sequence alignment.  I can easily get a list of peptides from compnovo, and I can use the Vernalis tool set to read in a FASTA database, but I don't know of a good tool to score the sequence similarities.  Can SeqAn do this?  I have had a hard time with the documentation (particularly in KNIME) and I haven't been able to find any workflows that show anything quite like this with SeqAn in KNIME. thank you! Lee -- ------- Lee S Parsons, PhD RIS Biological Mass Spectrometry Analyst | Minnesota Supercomputing Institute | www.msi.umn.edu University of Minnesta | umn.edu lparsons@umn.edu | 612-624-4466 --------------D8F677A1C7B430015628D563 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit


Hello

I would like to use SeqAn to align peptide sequences to protein (FASTA)
databases.  Is there a way to do this?

I work with a lot of proteomics data in KNIME, and the OpenMS group
suggested I look into SeqAn for what I'm trying to do next.  While you
probably know that the OpenMS project already has several spectral
matching search algorithms built in to it, the project only has one de
novo algorithm (compnovo).  While compnovo is a great tool, by virtue of
being a de novo algorithm it does not do sequence alignment.  I can
easily get a list of peptides from compnovo, and I can use the Vernalis
tool set to read in a FASTA database, but I don't know of a good tool to
score the sequence similarities. 

Can SeqAn do this?  I have had a hard time with the documentation
(particularly in KNIME) and I haven't been able to find any workflows
that show anything quite like this with SeqAn in KNIME.

thank you!
Lee
-- 
-------
Lee S Parsons, PhD
RIS Biological Mass Spectrometry Analyst | Minnesota Supercomputing Institute | www.msi.umn.edu
University of Minnesta | umn.edu
lparsons@umn.edu | 612-624-4466
--------------D8F677A1C7B430015628D563-- From hannes.hauswedell@fu-berlin.de Wed Nov 21 19:27:25 2018 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) 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 <1gPXDh-001AvN-6R>; Wed, 21 Nov 2018 19:27:25 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.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 <1gPXDh-0000Nv-33>; Wed, 21 Nov 2018 19:27:25 +0100 Received: from [160.45.38.134] (helo=celegans.imp.fu-berlin.de) by inpost2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtpsa (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1gPXDg-001F2P-Q4>; Wed, 21 Nov 2018 19:27:25 +0100 From: Hannes Hauswedell To: SeqAn Development Date: Wed, 21 Nov 2018 19:27:23 +0100 Message-ID: <1965491.uJW0cDvVUg@celegans.imp.fu-berlin.de> Organization: MPI MolGen / FU-Berlin In-Reply-To: <2a04c653-3839-1bde-e0be-735324ff26a6@umn.edu> References: <2a04c653-3839-1bde-e0be-735324ff26a6@umn.edu> MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" X-Originating-IP: 160.45.38.134 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1542824845-000004BE-F1C23413/0/0 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, T_FILL_THIS_FORM_SHORT,URIBL_BLOCKED X-Spam-Checker-Version: SpamAssassin 3.4.2 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] SeqAn for proteomics searches in KNIME? X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.29 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 21 Nov 2018 18:27:25 -0000 Am Dienstag, 20. November 2018, 21:59:45 CET schrieb Lee S Parsons: > Hello >=20 > I would like to use SeqAn to align peptide sequences to protein (FASTA) > databases. Is there a way to do this? >=20 > I work with a lot of proteomics data in KNIME, and the OpenMS group > suggested I look into SeqAn for what I'm trying to do next. While you > probably know that the OpenMS project already has several spectral > matching search algorithms built in to it, the project only has one de > novo algorithm (compnovo). While compnovo is a great tool, by virtue of > being a de novo algorithm it does not do sequence alignment. I can > easily get a list of peptides from compnovo, and I can use the Vernalis > tool set to read in a FASTA database, but I don't know of a good tool to > score the sequence similarities.=20 >=20 > Can SeqAn do this? I have had a hard time with the documentation > (particularly in KNIME) and I haven't been able to find any workflows > that show anything quite like this with SeqAn in KNIME. >=20 > thank you! > Lee Dear Lee, are you looking for a stand-alone tool? Have you tried Lambda, our protein= =20 alignment program? https://github.com/seqan/lambda I am afraid there is no KNIME integration, yet, but it would not be difficu= lt=20 to add. Best regards, Hannes =2D-=20 Hannes Hauswedell Scientific staff & PhD candidate =46reie Universit=C3=A4t Berlin / Max Planck Institute for Molecular Geneti= cs address Institut f=C3=BCr Informatik Takustra=C3=9Fe 9 Room 019 14195 Berlin telephone +49 (0)30 838-75241 fax +49 (0)30 838-75218 e-mail hannes.hauswedell@fu-berlin.de