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However, bioperl does provide a HMMER report parser. Alignment Objects Early versions used UnivAln, SimpleAlign Ver. 1.0 only support SimpleAlign.
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Includes set of regular expression & matching tools. Good string manipulation tool ... Local alignment program: Smith Waterman. Module : Bio::Tools::pSW. Sample Code: ...
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BioPerl Introduction by Hairong Zhao. BioPerl Script Examples ... Components of a module name are separated by double colons (::). For example, Math::Complex ...
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Bioperl modules. Object Oriented Programming in Perl (1) ... Components of a module name are separated by double colons (::). For example, Math::Complex ...
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An interpreted programming language that resembles both a real ... Commands to decompress and untar the bioperl file. All bioperl files are in this folder now ...
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On cygwin (Linux-like environment in Windows) Install cygwin. Install ... early in the installation through cygwin, double check the firewall settings on ...
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Goal: collect computational methods routinely used in bioinformatics ... bioinformatics toolkit for format conversion, report processing, data ...
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Cultural divide between biologists and computer science. use ... Unix, Linux, Windows, VMS... TIMTOWTDI. There Is More Than One Way To Do It. rot13 example ...
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BioPerl BioPerl BioPerl: the SeqIO module BioPerl: the Seq module Class exercise 14 BioPerl: Parsing a GenBank file BioPerl: Parsing a GenBank file BioPerl ...
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Download the perl script (new version) from the class web site ... Open the script with perl express or notepad (Windows users) or Text Wrangler (Mac users) ...
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bioperl - perl tools for Molecular biology biopython ... Python distribution tools DND - Protein molecular dynamics simulation/visualization DomainFinder ...
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Genes to Trees Daniel Ayres and ... Scripting will be done with Perl Extensive use of BioPerl libraries Collection of modules for bioinformatics programming ...
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The third Bioinformatics Open Source Conference, BOSC 2002. August 1-2, 2002, Edmonton, Canada ... heavily used in bioinformatics. Bioperl http://www.bioperl. ...
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(DHTML, Perl, CGI) Blast Output (BLASTN/P/X, TBLASTN/X) Perl Scripts (BioPerl Modules) ... (DHTML, Perl, CGI, Ajax) - Select Genomes - Query Sequences. BLAST ...
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Derived from genomics all the DNA in an organsim ... http://sial.org/howto/perl/life-with-cpan/non-root/ Bioperl annotation examples ...
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Search/Retrieval in Genome Information systems. Efficiency and complexity: ... Mouse GD, Sacc. GD (RDBMS) GeneCards (Glimpse XMLquery) Ensembl (RDBMS,BioPerls) ...
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Data sources. Sequencing technique. New on AFS! Bioperl (actually, this is old) Biopython ... Python Imaging Library, PIL (All in the same lib directory) biojava ...
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An Introduction to Perl for Bioinformatics Part 2. Will Hsiao ... Create web forms. Lecture 6.1. 9. Bioperl Overview. The Bioperl project www.bioperl.org ...
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de facto standard for bioinformatics researchers. BioPerl module ... May want to also consider Python. beginning to be used for Bioinformatics ...
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Title: PowerPoint Presentation Author: David Last modified by: Haim Created Date: 1/1/1601 12:00:00 AM Document presentation format (4:3)
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Title: PowerPoint Presentation Last modified by: iand Document presentation format: On-screen Show (4:3) Other titles: Times New Roman Arial Comic Sans MS Courier New ...
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Title: PowerPoint Presentation Last modified by: Ian Donaldson Created Date: 1/1/1601 12:00:00 AM Document presentation format: On-screen Show (4:3)
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Data mining. Select direct. access. SOAP. Analysis. execution ... XML data. etc. Web Services. Description Language. WSDL. XML linking? Life Sciences Identifier ...
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Porting CHADO and GMOD Tools to Oracle and Integration with dictyBase Eric Just dictyBase http://dictybase.org Center for Genetic Medicine Northwestern University
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Title: Slide 1 Author: aday Last modified by: Scott Cain Created Date: 3/25/2005 1:13:05 AM Document presentation format: On-screen Show Company: Affymetrix, Inc
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Title: BioRuby : in-house R&D Author: ayu Last modified by: ayu Created Date: 1/10/2002 1:53:35 AM
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Sequence Alignment
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... its easy for the programmers Open Source Bioinformatics Almost all of the bioinformatics software that you need to do ... multiple alignment Phylip ...
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Most popular on Unix/Linux systems. Excellent language for file and data processing ... Yes, there is documentation, but it can be difficult to see the big picture' ...
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Want to use CHADO for feature data, but dicty' SGD schema for the rest ... Object name limited to 30 characters, systematically truncate names ...
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Differential insertion of transposable elements in Anopheles gambiae M & S genomes Jenica L. Abrudan, Ryan C. Kennedy, Maria F. Unger, Michael R. Olson, Scott J ...
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Bioinformatics Open Source Conference, June 23-24 2005, Detroit. What's BioRuby? ... Bug fixes. We will not continue to support Ruby 1.6. RubyGems for easy ...
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Funny? Goals. I already assume you know perl basics -- some more advanced features ... Regular expressions, text manipulations. Extensions (modules) do this ...
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Nucleotide sequence is 3 X longer than protein sequence. ... Hydrophobicity. Containing no polar side chains. Interact less favorably with water ...
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Genomes, maps, stocks, phenotypes, anatomies, pathways, ... Worm, fly, yeast, mouse, arabidopsis, rat. Funded by NIH as of June 2002. http://www.gmod.org ...
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Using Hidden Markov Models to finding gene in DNA sequences ... ??????????? ??????? Bioinformatics ?? ???? ?????? ?????? ????? ?????????? (????? ...
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Data retrieval BioMart Export View Data sets on ftp site MySQL queries of databases Perl API access to databases Data Mining in Ensembl with EnsMart Possible queries
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An Introduction to Perl for bioinformatics
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There are two extremes in bioinformatics work ... Sociobiology Psychology. Systems Biology. Biology Medicine. Molecular Biology. Chemistry ...
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Ian Holford (Molecular and Cellular Imaging Center) Xiaodong Bai (Entomology) http://www.oardc.ohio-state.edu/tomato/ Survey: HCS806SurveyPre.doc ...
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ENGINEERING GOAL: Improve global access to bioinformatics data, tools, and resources. ... Allow biologists to easily discover and run bioinformatics tools ...
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Italy generated brilliant scientists, but lagged in ... Damian Gessler, Wednesday 4:15 pm, Canyon IV. http://www.biomoby.org. Moving Towards Nationhood ...
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COSMIC GBrowse Visualising cancer mutations in genomic context Dave Beare dmb@sanger.ac.uk Cancer Genome Project Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
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Practice retrieving data and running stand alone BLAST. ... Solanum pennellii (EST) Query: Select Pathway by name. Enter: Abscisic Acid. Submit ...
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Why do I need to know how to program?' Know your field, and your data ... programming languages - Perl, Python, C, C , Java, Visual Basic, PHP ...
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Data Mining for Bioinformatics. Craig A. Struble, Ph.D. Marquette University ... Bioinformatics data. Survey of KDD steps. Case Study: miRNA Project ...
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It prints: The probe at row 1, column 2 has value 8 ... This prints out: Amino acids 1. E V L D T Y. Amino acids 2. Passing References to Subroutines ...
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Author of 'Beginning Perl for Bioinformatics' and 'Mastering Perl for ... PRI: primate sequences. ROD: rodent sequences. PHG: bacteriophage sequences ...
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A community-based approach to bioinformatics analysis ... Mauve. LAGAN. DIALIGN. Conreal. ClustalW. Future Plans. Acknowledgements. GENOME SCIENCES CENTRE ...
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Chado and interoperability Chris Mungall, BDGP Pinglei Zhou, FlyBase-Harvard
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Peer-to-peer bioinformatics. iCapture Lunch and Learn' November 2004. Stephen Montgomery ... Avoiding empty text boxes database type ENSEMBL /type ...
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To facilitate context-driven hypotheses on the function of non-coding polymorphisms ... ORCA. Mauve. LAGAN. DIALIGN. Conreal. ClustalW. Projects involving Chinook ...
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An interaction map of biologists and bioinformaticians. Things ... Wyeth Wasserman. Jonathan Lim. UBC BIOINFORMATICS CENTRE. Francis Ouellette. Graham McVicker ...
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Used to retrieve data from and store data in the Ensembl ... Acknowledgements. The Ensembl Core Team. Glenn Proctor. Andreas Kahari. Daniel Rios. Ian Longden ...
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Learn one middleware, use on many projects. More efficient use of time. Adds a do-it-yourself aspect to GMOD. Makes extending/customizing easier. Middlware Approaches ...
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