University of Belgrade School of Electrical Engineering Implementation

University of Belgrade School of Electrical Engineering Implementation of the BLAST Algorithm Using Hadoop Map. Reduce Siniša Ivković, Goran Rakočević, Prof. Veljko Milutinovic

Introduction -Sequence alignment • way of arranging sequences of DNK, RNK or protein to identify regions of similarity • • • functional structural evolutionary relationships between sequences - How to know that two genes, often in different organizams, in fact two versions of the same gene? Similarity! Siniša Ivković - sinisa. ivkovic@gmail. com 2/13

Introduction • There a number of algorithms that solve problems of aligning the sequences and guarantee the best solutions • By increasing amount of data that need to be processed execution speed of these algorithms becomes unacceptable • Therefore, we must turn to heuristic methods - BLAST Siniša Ivković - sinisa. ivkovic@gmail. com 3/13

BLAST - Basic Local Alignment Search Tool • Fast local sequence alignment algorithm • BLAST efficiency lies in the fact that it tends to find regions of high similarity, not necessarily trying to find and check all local alignment. KRKLQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL KKKHRRNRTTFTTYQLHQLERAFEASHYPDVYSREELAAKVHLPEVRVQVWFQNRRAKWRRQERL Siniša Ivković - sinisa. ivkovic@gmail. com 4/13

Parallel BLAST - Most bioinformatics algorithms are designed as a sequential • The very nature of bioinformatics processing • The rapid spread of knowledge in biology causes constant emergence of new concepts, and significant changes to already known - Declining price of genome sequencing requires increasing the speed of execution of these algorithms - Implementations of Parallel BLAST • PThread • MPI Siniša Ivković - sinisa. ivkovic@gmail. com 5/13

ETF Hadoop BLAST - Big Data – collection of data sets so large and complex that it becomes difficult to process using standard database tools or traditional data processing applications - Parallel computing – a form of computation in which many calculations are carried out simultaneously • communication and synchronization between processes • hardware failure - Map. Reduce – programming model that frees programmers of thinking about these problems - Apache Hadoop – free implementation of the Map. Reduce paradigm Siniša Ivković - sinisa. ivkovic@gmail. com 6/13

Map. Reduce VALUE MAP SORT VALUE REDUCE VALUE MAP REDUCE VALUE Siniša Ivković - sinisa. ivkovic@gmail. com 7/13

ETF Hadoop BLAST - Implementation my. Sequence {db 1} {q 1} {db 2} {db 3} {q 1} {db 1} {q 1} MAP {db 2} {q 1} MAP {db 3} MAP {hit 1} {db 1} {hit 3} {db 2} {hit 5} {db 3} {hit 2} {db 1} {hit 4} {db 2} {hit 6} {db 3} Siniša Ivković - sinisa. ivkovic@gmail. com 8/13

my. Sequence {q 1} {db 2} {db 3} ETF Hadoop BLAST - Implementation {q 1} {db 1} {q 1} MAP {db 2} {q 1} MAP {db 3} MAP {hit 1} {db 1} {hit 3} {db 2} {hit 5} {db 3} {hit 2} {db 1} {hit 4} {db 2} {hit 6} {db 3} REDUCE {hit 1} {db 1} {hit 3} REDUCE {db 2} {hit 6} Siniša Ivković - sinisa. ivkovic@gmail. com {db 3} 9/13

ETF Hadoop BLAST >GENSCAN 0000013 pep: genscan chromosome: GRCh 37: 18: 4755977: 4807982: 1 transcript: GENSCAN 0000013 transcript_biotype: protein_coding TANTGLLAVKVEVIILVSLTHAQLSRAGQHAGCTTCLQDECAVAAGEEEETQQGELADVIYPSL LAASTSSVLEDGAGPHKGLQKLSRLIRFVDVVGGFRREKGYMAWIKPRYSEFPKVNSWTESSF PFG HSP: 661 E-value: 0. 001446314485823671 Siniša Ivković - sinisa. ivkovic@gmail. com 10/13

Conclusion - Bioinformatics has become an important part of many areas of biology • • • Sequencing and annotating genomes and their observed mutations Datamining of biological literature and the development of gene ontologies Understanding of evolutionary aspects of molecular biology - Personalized medicine • Medical model that proposes the customization of healthcare • We need to consider whole spectar of clinical information • Electronic health care records • Clinical trials • etc. Siniša Ivković - sinisa. ivkovic@gmail. com 11/13

Conclusion - We need to collect information from real world - Develop analytics that can actually extract causal relationships and generate predictive models - Future steps: - Specialized hardvare (FPGA) Siniša Ivković - sinisa. ivkovic@gmail. com 12/13

Thank you for your attention Siniša Ivković sinisa. ivkovic@gmail. com 13/13