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MBG305 Applied Bioinformatics

MBG305 Applied Bioinformatics. Week 2 (02.10.2010) Jens Allmer. Quiz. 10 min. Databases. Bioinformatics needs data Where is this data? Is there any organization? How should I cite data?. Where is the data?. Many targeted resources exist miRBase http://www.mirbase.org/

1.07k views • 72 slides

MBG305 Applied Bioinformatics

MBG305 Applied Bioinformatics. Week 2 (05.10.2010) Jens Allmer. Databases. Bioinformatics needs data Where is this data? Is there any organization? How should I cite data?. Where is the data?. Many targeted resources exist miRBase http://www.mirbase.org/ Contains microRNAs

843 views • 70 slides

Welcome to lecture 2: Feeling at home in *nix

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Gene Prediction

Gene Prediction. Preliminary Results Computational Genomics February 20, 2012. ab initio Gene Prediction. Using Glimmer3, RAST, Prodigal and GenemarkS. Prodigal. lack of complexity(no Hidden Markov Model, no Interpolated Markov Model). based on dynamic programming.

756 views • 49 slides

Basic Introduction of BLAST

Basic Introduction of BLAST. Jundi Wang School of Computing CSC691 09/08/2013. Overview. 1.Introduction of BLAST Background of BLAST Programs in BLAST Function of BLAST 2.Application of BLAST BLAST web version Stand-alone BLAST. Background of BLAST.

1.88k views • 31 slides

Biological Databases and Tools

Biological Databases and Tools. Sandra Sinisi / Kathryn Steiger November 25, 2002. Introduction. More than storage Qualities of a good database Flexible retrieval Analysis software compatible Data cleaning features. The need for electronic access.

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Multiple Sequence Alignments

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More loops

More loops. Commands inside a loop are executed repeatedly (iteratively): my $num=0; print "Guess a number. "; while ($num != 31) { $num = <STDIN>; } print "correct! ";. Loops. my @names = <STDIN>; chomp(@names); my $name; foreach $name (@names) { print "Hello $name! "; }.

315 views • 22 slides

Perl Programming: Developing Key Tools for Bioinformatics

Perl Programming: Developing Key Tools for Bioinformatics. An Informative Look Behind the Importance of Programming Skills and Brief Tutorial on Getting Started With Perl and Bioperl. Andrew C. Rieser 4-1-04. Why Computer Skills are Important.

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SMARTAR: small RNA transcriptome analyzer

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Christian Rinke Microbial Genomics DOE, Joint Genome Institute crinke@lbl

Introduction to ARB (From A User's Perspective). Christian Rinke Microbial Genomics DOE, Joint Genome Institute crinke@lbl.gov. Reasons for using molecular markers. Sort and classify organisms. Unravel evolutionary relationships. Track back the origin of organisms.

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File formats and conversions

File formats and conversions. Important formats. How Fasta Raw/Peptide Tab. How. One or more entries First line Length of sequence (6 digits right aligned) Name of sequence Next lines Sequence, usually 80 characters pr line Last lines Assignments of the positions in the sequence.

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SARS: A Multidisciplinary Exploration

SARS: A Multidisciplinary Exploration . Nitya Jacob Doug Graham Eloise Carter Manish Chakrabarti. Teaching with an Epidemic. SARS as a topic to introduce problem solving in biology, medical epidemiology and bioinformatics Diverse sources of information on SARS used to introduce the topic

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Parsing XML sequence?

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More loops

More loops. Commands inside a loop are executed repeatedly (iteratively): my $num=0; print "Guess a number. "; while ($num != 31) { $num = <STDIN>; } print "correct! ";. Loops. my @names = <STDIN>; chomp(@names); my $name; foreach $name (@names) { print "Hello $name! "; }.

216 views • 14 slides

Iteration

Iteration . While / until/ for loop. While/ Do-while loops . Iteration continues until condition is false: 3 important points to remember: Initialise condition variable, A correct condition expression , change condition variable while-loops : #!/ usr/bin/perl $count = 1; #1

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OUTPUT

FSTs in FASTA format. PHD format FASTA format FASTQ format. Check Sequence Quality. T-DNA Adaptor Vector. INPUT. VALIDATING. FSTs Validating result (A, NA, Vector, or Low) Masked FSTs. Check similarities and positions of T-DNA, Adaptor and Vector in a FST. MAPPING.

146 views • 1 slides