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IEETA seminar of Diogo Pratas, July 2017


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Title Compression-based ancient DNA analysis
Speaker Diogo Pratas
Institution IEETA
Date 2017/07/21
Time 11h00
Location Anfiteatro do IEETA
Country Portugal

Abstract: We propose an automatic system for ancient DNA analysis that integrates several tools in a circular dynamic map architecture. These tools are mainly based on data compression. The system uses relative compressors to estimate the relative similarity between genomes. These compressors allow unsupervised and alignment-free data mining, avoiding several hurdles that other methods have to face. Unlike alignment-based methods, the compressors run with linear time complexity and generate conservative results.

The system is able to perform: (1) automatic search and download of ancient sequenced reads from the web (2) identification and filtering of sequencing artifacts from the reads ; (3) inference of the metagenomic sample composition, including the elimination of false positives given by cross-similarity within the database; (4) classification of microorganisms: ancient or contamination; (5) assembly of ancient host and pathogen genomes; (6) analysis between ancient and modern-days similar species; (7) generate reports and add knowledge to next runs;