Paper Details: Downloads: 544
Serial Number: P1161137804
Title: A New Presentation Method of Nucleotide Sequences Minimizes Storage Size and Processing Time
Authors: Nahed H. Solouma
Abstract: The biological databases have a vast amount of data representing the sequences of genomes, genes and proteins of different species. Another related and/or deduced information such as protein structures and protein-protein interactions are also present. The number of sequences and the related information are drastically increasing. This deluge of data creates great challenges to computer scientists to store and process the so long sequences efficiently. We proposed a new method for nucleotide sequence encoding. Our encoding method is based on the fact that there are only four nucleotide bases i.e. four different states. Any sequence can be segmented to four-bases segments and hence, we have only 256 combinations to represent any sequence. The code of any sequence is thus a sequence of numbers ranging from 0-255. We named the new sequence code as 4-into-1 code. Many sequences were encoded using the proposed encoding method which saves 75% of the storage capacity. The most common sequence analysis algorithms were modified and redesigned to be suitable for the application to the 4-into-1 codes. Surprisingly, the computation complexity and hence the calculation time are greatly reduced using our proposed methods. Using the 4-into-1 code, the computation complexity of the dot plots and global sequence alignment are reduced to one sixteenth of its original complexity. Dynamic programming can be efficiently applied to the 4-into-1 code for local sequence alignment. The palindrome regions in a sequence are easily obtained using the 4-into-1 code. The 4-into-1 code can be used to numerically represent the nucleotide sequence and hence, signal processing algorithms can be applied efficiently.
Keywords: compression, Nucleotide sequences, numerical representation.
Journal/Conference: ICGST Conference on Computer Science and Engineering, CSE-11
Volume:
Issue:
Submission Date: 9/15/2011 12:00:00 AM
Review Date: 11/22/2011 2:22:43 PM
Publishing Date: 12/19/2011 12:00:00 AM
Article Downloads: 544
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