lecture-5 - Practical Bioinformatics for Life Scientists...

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Practical Bioinformatics for Life Scientists Week 3, Lecture 5 István Albert Bioinformatics Consulting Center Penn State
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Processing sequencing reads Sequenced DNA fragments (DNA library) Unknown genome De novo assembly (contigs) Read mapping (alignments) gene discovery (annotation) Known genome (reference) chip-Seq, RNA-Seq, SNP calling etc.
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Sequence alignments Arranging two or more sequences such as to maximize the length of the common regions between the two It is a very well developed field the roots of the bioinformatics started with various alignment software We will only cover pair-wise alignments searching a database with a query High throughput sequencing poses special constraints: a very large number of very short reads - traditional methods were not feasible
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Alignment concepts A GCAAG TAT GTAAG GGC GCAG AAAA GCAAAG GCAAG GCAAG perfect match one mismatch GCAAG GCAAG insertion vs ref. deletion vs ref
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This note was uploaded on 02/29/2012 for the course BMMB 597D taught by Professor Istvanalbert during the Fall '11 term at Pennsylvania State University, University Park.

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lecture-5 - Practical Bioinformatics for Life Scientists...

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