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Searching the Referentially-compressed Genomes by Incomplete Patterns

by Mohammad Nassef, Amr Badr, Ibrahim Farag
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International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 88 - Number 1
Year of Publication: 2014
Authors: Mohammad Nassef, Amr Badr, Ibrahim Farag
10.5120/15313-3624

Mohammad Nassef, Amr Badr, Ibrahim Farag . Searching the Referentially-compressed Genomes by Incomplete Patterns. International Journal of Computer Applications. 88, 1 ( February 2014), 1-8. DOI=10.5120/15313-3624

@article{ 10.5120/15313-3624,
author = { Mohammad Nassef, Amr Badr, Ibrahim Farag },
title = { Searching the Referentially-compressed Genomes by Incomplete Patterns },
journal = { International Journal of Computer Applications },
issue_date = { February 2014 },
volume = { 88 },
number = { 1 },
month = { February },
year = { 2014 },
issn = { 0975-8887 },
pages = { 1-8 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume88/number1/15313-3624/ },
doi = { 10.5120/15313-3624 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T22:06:27.967423+05:30
%A Mohammad Nassef
%A Amr Badr
%A Ibrahim Farag
%T Searching the Referentially-compressed Genomes by Incomplete Patterns
%J International Journal of Computer Applications
%@ 0975-8887
%V 88
%N 1
%P 1-8
%D 2014
%I Foundation of Computer Science (FCS), NY, USA
Abstract

Genome banks contain precious biological information that is mostly not discovered yet. Biologists in turn are keen to precisely explore these banks in order to discover effective patterns (such as motifs and retro-transposons) that have a real impact on the function and evolution of living creatures. Because the modern genome sequencing technologies produce genomes in high throughputs, many techniques have emerged to store genomes in the lowest possible space. Reference-based Compression algorithms (RbCs) efficiently compress the sequenced genomes by mainly storing their differences with respect to a reference genome. Therefore, RbCs give very high compression ratios compared to the traditional compression algorithms. However, in order to search a compressed genome for specific patterns, it has to be totally decompressed, wasting both time and storage. This paper introduces searching for either exact or incomplete patterns inside the referentially compressed genomes without their complete decompression. The introduced search methodolgy is based on instantly searching subsequent sequences that are partially decompressed from the compressed genome. Moreover, the same search process is allowed to simultaneously search for multiple patterns, thus saving more resources. The experimental results showed noticeable performance gains compared to traditionally searching the same compressed genomes after their complete referential decompression.

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Index Terms

Computer Science
Information Sciences

Keywords

Reference-based Genome Compression Partial Genome Decompression Searching Compressed Genome Incomplete Patterns inCompressi.

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