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lecture13_slides

# lecture13_slides - Midterm 1 grade summary > = 74 >= 72 >=...

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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
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
Introduction to gene expression microarray technology Chad Myers Department of Computer Science and Engineering University of Minnesota [email protected] 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