From N.H.Mann at warwick.ac.uk Thu Sep 15 07:31:15 2005 From: N.H.Mann at warwick.ac.uk (Nick Mann) Date: Thu, 15 Sep 2005 12:31:15 +0100 Subject: [Bio-Linux] Bio-Linux packages: OligoArray and muscle Message-ID: Hi Bela, This link is to a program that could be a very useful addition to Biolinux http://www.ebi.ac.uk/goldman/prank/ Best wishes Nick Professor Nicholas H. Mann Department of Biological Sciences University of Warwick Coventry CV4 7AL UK Tel: +44 (0)2476 523526 Fax +44 (0)2476 523701 From btiwari at ceh.ac.uk Thu Sep 15 11:35:57 2005 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Thu, 15 Sep 2005 16:35:57 +0100 Subject: [Bio-Linux] Bio-Linux package for prank: multiple alignment software Message-ID: Hello The new multiple alignment software "prank" is now packaged for Bio-Linux. Thanks to Nick Mann for recommending this software. The web page for this software is: http://www.ebi.ac.uk/goldman/prank/ To quote from the abstract of their paper: "We describe a modification of the traditional alignment algorithm that can distinguish insertion from deletion and avoid repeated penalization of insertions and illustrate this method with a pair hidden Markov model that uses an evolutionary scoring function. In comparison with a traditional progressive alignment method, our algorithm infers a greater number of insertion events and creates gaps that are phylogenetically consistent but spatially less concentrated. Our results suggest that some insertion/deletion "hot spots" may actually be artifacts of traditional alignment algorithms." Reference: Loytynoja A, Goldman N. 2005 An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci U S A. Jul 26;102(30):10557-62. Please note that prank is still under development and the authors note on their website that there may be bugs and there is currently no error checking. We are on their mailing list and will edeavor to update the bio-linux package whenever we receive alerts from the developers. Some sample instructions for how to run the software can be found in the README file at /usr/local/bioinf/prank/prank/README or on the website given above. The bio-linux-prank package can be installed using Synaptic. This software will not be installed automatically although it will be kept updated after it is initially installed. Some information about how to do this can be found at: http://envgen.nox.ac.uk/envgen/software/archives/000503.html#Synaptic cheers Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any views or opinions expressed are those of the author and do not represent the views of NERC unless otherwise explicitly stated. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and your reply cannot be guaranteed. From asmo at ceh.ac.uk Mon Sep 19 04:46:27 2005 From: asmo at ceh.ac.uk (Ashley Morley) Date: Mon, 19 Sep 2005 09:46:27 +0100 Subject: [Bio-Linux] Envgen.nox.ac.uk webserver downtime today 19 Sept 2005. Message-ID: Dear Colleagues, Please be aware that at 3.30pm today the envgen.nox.ac.uk webserver will be off-line for approximately 20-30 minutes. We will notify you as soon as it is back on-line. Thank you for your patience. Kind regards Ashley Morley Ashley Morley, Technical Administrator NEBC (formerly EGTDC), Centre for Ecology & Hydrology Mansfield Road, Oxford, OX1 3SR UK Tel: +44 (0) 1865 281976 Fax: +44 (0) 1865 281 696 http://envgen.nox.ac.uk/ Email: asmo at ceh.ac.uk This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any views or opinions expressed are those of the author and do not represent the views of NERC unless otherwise explicitly stated. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and your reply cannot be guaranteed. From asmo at ceh.ac.uk Mon Sep 19 11:12:15 2005 From: asmo at ceh.ac.uk (Ashley Morley) Date: Mon, 19 Sep 2005 16:12:15 +0100 Subject: [Bio-Linux] NEBC webserver back online. Message-ID: Dear Colleagues, The NEBC (formerly EGTDC) website server is now back online after it's brief journey around the building at CEH! Kind regards Ashley Ashley Morley, Technical Administrator NEBC (formerly EGTDC), Centre for Ecology & Hydrology Mansfield Road, Oxford, OX1 3SR UK Tel: +44 (0) 1865 281976 Fax: +44 (0) 1865 281 696 http://envgen.nox.ac.uk/ Email: asmo at ceh.ac.uk This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any views or opinions expressed are those of the author and do not represent the views of NERC unless otherwise explicitly stated. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and your reply cannot be guaranteed. From btiwari at ceh.ac.uk Mon Sep 26 12:02:00 2005 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Mon, 26 Sep 2005 17:02:00 +0100 Subject: [Bio-Linux] new and updated packages for Bio-Linux Message-ID: Hello, This is just an update about packages available for Bio-Linux: 1) bio-linux-blast has been udpated and contains ncbi blast version 2.2.12. 2) bio-linux-emboss has been updated and contains version 3.0.0. This package checks if you have a file called /usr/local/bioinf/EMBOSS/EMBOSS/emboss/emboss.default. If you do, it will be saved during the installation and put back afterwards. Thus, any database specific information you have added should not be lost. For those of you how have never looked at this file - you can specify remote and local database access methods and locations that allow users to access sequence (and related) files using EMBOSS programs such as seqret. The default version in the bio-linux-emboss package specifies embl, swissprot and trembl (aka uniprot) and refseq from the ebi. Genbank is also specified - from infobiogen in France. All are accessed using srs. 3) A new package called bio-linux-clcworkbench is available. This contains version 1.01 of the CLCFreeWorkBench from CLCbio. Information about this package is available here: http://www.clcbio.com/index.php?area=software§ion=free At the moment, I would encourage you to try out this package before suggesting to all your users that they use it. It looks like it has great potential and we would be grateful for any feedback about it if anyone tries it out. Of particular interest is the fact that the people developing this intend it to be the base for an extended package that would be able to handle a wider range of sequence analysis tasks. After installation, the software can be started up by typing "clcwb" or "clcworkbench" on the command line. The EMBOSS and blast packages will be updated automatically on your machines tonight (assuming you leave your machine on and have not chosen to disable the automatic updating facility). bio-linux-clcworkbench can be installed using synaptic. Information about installing packages using synaptic can be found here: http://envgen.nox.ac.uk/envgen/software/archives/000503.html#Synaptic cheers Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any views or opinions expressed are those of the author and do not represent the views of NERC unless otherwise explicitly stated. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and your reply cannot be guaranteed.