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Sequence Alignment technology. Chengwei Lei Fang Yuan Saleh Tamim. Goal. Save time “PASS : a Program to Align Short Sequences Davide Campagna et al . Bioinformatics (2009 )” Save money - PowerPoint PPT Presentation

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Alignment

Sequence Alignment technologyChengwei LeiFang YuanSaleh Tamim

GoalSave timePASS: a Program to Align Short SequencesDavide Campagna et al. Bioinformatics (2009)

Save moneyOptimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies, Iman Hajirasouliha, Bioinformatics (2008)Keywords in both paperReference sequence: A long Genomic sequence.

Short reads: Input short strings. e.g. ATGCGTACSave time PASS programPASS, a new algorithm to align short DNA sequences allowing gaps and mismatches.The performance of the program is very striking both for sensitivity and speed. For instance, gap alignment is achieved hundreds of times faster than BLAST and several times faster than SOAP, especially when gaps are allowed.PASS Program to Align Short Sequences Performs gapped and ungapped alignment onto a reference sequence Seed words (11 and 12 bases) Short reads (7 and 8 bases) PST - calculated with the Needleman and Wunsch algorithm supplied with PASS Handles data generated by Solexa, SOLiD or 454 technologies

Approach/Algorithm

Analysis and ResultsComparison of PASS with SOAP

PASS has better sensitivity with words of 11 and runs at least 10 times faster

Sensitivy increases7Save money - Optimal pooling methodA set of experiments using the Solexa technology, based on bacterial artificial chromosome (BAC) clones, and address an experimental design problem.

Basic idea: More than one BAC per lane in order to maximize the throughput of the Solexa technology, hence minimize its cost.Input strings (short reads)Reference sequencesInputsNormal pooling methodOne other hurdle in designing a globally optimal experiment is the rapid proliferation of number of possible configurations. For instance, if we would like to pool m=150 BACs into 15 groups of size=10, we would need to consider

Infeasible to search all these configurationsOptimal Pooling methodInput strings (short reads)Reference sequenceOptimal Pooling methodInput strings (short reads)Reference sequencesOptimal Pooling methodInput strings (short reads)Reference sequencesOptimal Pooling methodPoolProblemHow to separate the groups of short reads?

Input strings (short reads)Reference sequenceOptimal Pooling methodPoolTwo cases

Result

17ConclusionProgram for Save timePASS: a Program to Align Short SequencesDavide Campagna et al. Bioinformatics (2009)

Algorithm for Save moneyOptimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies, Iman Hajirasouliha, Bioinformatics (2008)Q & A