ProtPCV: A Fixed Dimensional Numerical Representation of Protein Sequence to Significantly Reduce Sequence Search Time.

Interdisciplinary Sciences, Computational Life Sciences
Manoj Kumar PalRajnish Kumar

Abstract

Protein sequence is a wealth of experimental information which is yet to be exploited to extract information on protein homologues. Consequently, it is observed from publications that dynamic programming, heuristics and HMM profile-based alignment techniques along with the alignment free techniques do not directly utilize ordered profile of physicochemical properties of a protein to identify its homologue. Also, it is found that these works lack crucial bench-marking or validation in absence of which their incorporation in search engines may appears to be questionable. In this direction this research approach offers fixed dimensional numerical representation of protein sequences extending the concept of periodicity count value of nucleotide types (2017) to accommodate Euclidean distance as direct similarity measure between two proteins. Instead of bench-marking with BLAST and PSI-BLAST only, this new similarity measure was also compared with Needleman-Wunsch and Smith-Waterman. For enhancing the strength of comparison, this work for the first time introduces two novel benchmarking methods based on correlation of "similarity scores" and "proximity of ranked outputs from a standard sequence alignment method" between all possible ...Continue Reading

References

Nov 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·S Henikoff, J G Henikoff
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Apr 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·W R Pearson, D J Lipman
Nov 1, 1966·Journal of Theoretical Biology·P H Sneath
Mar 1, 1970·Journal of Molecular Biology·S B Needleman, C D Wunsch
May 5, 1982·Journal of Molecular Biology·J Kyte, R F Doolittle
Mar 25, 1981·Journal of Molecular Biology·T F Smith, M S Waterman
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Apr 9, 1999·Protein Engineering·B Rost
May 29, 2000·Trends in Genetics : TIG·P RiceA Bleasby
Jan 16, 2002·Protein Science : a Publication of the Protein Society·Anna R Panchenko, Stephen H Bryant
Mar 4, 2003·Bioinformatics·Susana Vinga, Jonas Almeida
Jun 28, 2005·Nucleic Acids Research·Lukasz JaroszewskiAdam Godzik
Feb 24, 2009·Proceedings of the National Academy of Sciences of the United States of America·A Biegert, J Söding
Oct 14, 2009·BMC Bioinformatics·Van Hoa Nguyen, Dominique Lavenier
Mar 19, 2013·PloS One·Anna KaznadzeyDenis Kaznadzey
Jun 12, 2013·Current Protocols in Bioinformatics·William R Pearson
Dec 9, 2014·Computers in Biology and Medicine·Zhao-Hui QiJun Feng
Jan 31, 2016·Interdisciplinary Sciences, Computational Life Sciences·Rajnish KumarManoj Kumar Pal
Apr 7, 2016·Annual Review of Analytical Chemistry·Gloria M SheynkmanLloyd M Smith
Oct 5, 2017·Genome Biology·Andrzej ZielezinskiWojciech M Karlowski
Oct 17, 2017·Nature Biotechnology·Martin Steinegger, Johannes Söding
Nov 23, 2017·BMC Bioinformatics·Hongwei GeJinghong Yu
Jul 28, 2019·Genome Biology·Andrzej ZielezinskiWojciech M Karlowski

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Software Mentioned

MATLAB
FAST
RAFTS3
BLASTP
All FASTA
EMBOSS Open Software Suite
BLOcks
BLAST
PSI
ProtPCV

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