lecture13_slides

lecture13_slides - Midterm 1 grade summary > = 74 >=...

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Mean: ~ 70/80 Max: 80/80 Min: 33/80 > = 74 A >= 72 A- >= 70 B+ >= 66 B >= 64 B- >= 62 C+ >= 58 C >= 56 C- >= 54 D+ >= 50 D >= 48 D- Midterm 1 grade summary
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A collection of Perl modules for processing data for the life sciences A project made up of biologists, bioinformaticians, computer scientists An open source toolkit of building blocks for life sciences applications Supported by Open Bioinformatics Foundation (O|B|F), http://www.open-bio.org/ Collaborative online community Info from: http://www.ebi.ac.uk/~lehvasla/bioperl/BioperlOverview.html A brief overview of bioPerl
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Simple example #!/usr/bin/perl -w use strict; use Bio::SeqIO; my $in = new Bio::SeqIO(-format => 'genbank', -file => 'AB077698.gb'); while ( my $seq = $in->next_seq ) { print "Sequence length is ", $seq->length(), "\n"; my $sequence = $seq->seq(); print "1st ATG is at ", index($sequence,'ATG')+1, "\n"; print "features are: \n"; foreach my $f ( $seq->top_SeqFeatures ) { printf(" %s %s(%s. .%s)\n", $f->primary_tag, $f->strand < 0 ? 'complement' : '', $f->start, $f->end); } } Simple example, output % perl ex1.pl Sequence length is 2701 1st ATG is at 80 features are: source (1. .2701) gene (1. .2701) 5'UTR (1. .79) CDS (80. .1144) misc_feature (137. .196) misc_feature (239. .292) misc_feature (617. .676) misc_feature (725. .778) 3'UTR (1145. .2659) polyA_site (1606. .1606) polyA_site (2660. .2660) Info from: http://www.ebi.ac.uk/~lehvasla/bioperl/BioperlOverview.html
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Where to go if you’re interested http://docs.bioperl.org/ (see the “Tutorials” section to get started) Info from: http://www.ebi.ac.uk/~lehvasla/bioperl/BioperlOverview.html
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Introduction to gene expression microarray technology Chad Myers Department of Computer Science and Engineering University of Minnesota cmyers@cs.umn.edu CSCI3003: Introduction to Computing in Biology
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Sequencing enabled many more genomic technologies ( adapted from Charles Mallery , http://fig.cox.miami.edu/~cmallery/150/gene/sf13x1.jpg ) • Gene and protein expression • Protein-protein interactions • Tissue/cellular localization • Genetic interactions
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( adapted from Charles Mallery , http://fig.cox.miami.edu/~cmallery/150/gene/sf13x1.jpg ) Huh, W- K et al. Nature 425, 686−691 (2003). Nucleus Nuclear Periphery Endoplasmic Retic. Bud Neck Mitochondria Lipid particles Protein localization What else can we measure?
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( adapted from Charles Mallery , http://fig.cox.miami.edu/~cmallery/150/gene/sf13x1.jpg ) Samples Garber, Troyanskaya et al. Diversity of gene expression in adenocarcinoma of the lung. PNAS 2001, 98(24):13784-9.
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This note was uploaded on 10/21/2011 for the course CSCI 3003 taught by Professor Staff during the Spring '08 term at Minnesota.

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lecture13_slides - Midterm 1 grade summary &gt; = 74 &gt;=...

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