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Image Correlation Method for DNA Sequence Alignment

The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequ...

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Autores principales: Curilem Saldías, Millaray, Villarroel Sassarini, Felipe, Muñoz Poblete, Carlos, Vargas Vásquez, Asticio, Maureira Butler, Iván
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384675/
https://www.ncbi.nlm.nih.gov/pubmed/22761742
http://dx.doi.org/10.1371/journal.pone.0039221
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author Curilem Saldías, Millaray
Villarroel Sassarini, Felipe
Muñoz Poblete, Carlos
Vargas Vásquez, Asticio
Maureira Butler, Iván
author_facet Curilem Saldías, Millaray
Villarroel Sassarini, Felipe
Muñoz Poblete, Carlos
Vargas Vásquez, Asticio
Maureira Butler, Iván
author_sort Curilem Saldías, Millaray
collection PubMed
description The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were “digitally” obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs) and 100 scenes represented by 100 x 100 images each (in total, one million base pair database) were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%), specificity (98.99%) and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment.
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spelling pubmed-33846752012-07-03 Image Correlation Method for DNA Sequence Alignment Curilem Saldías, Millaray Villarroel Sassarini, Felipe Muñoz Poblete, Carlos Vargas Vásquez, Asticio Maureira Butler, Iván PLoS One Research Article The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were “digitally” obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs) and 100 scenes represented by 100 x 100 images each (in total, one million base pair database) were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%), specificity (98.99%) and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment. Public Library of Science 2012-06-27 /pmc/articles/PMC3384675/ /pubmed/22761742 http://dx.doi.org/10.1371/journal.pone.0039221 Text en Curilem et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Curilem Saldías, Millaray
Villarroel Sassarini, Felipe
Muñoz Poblete, Carlos
Vargas Vásquez, Asticio
Maureira Butler, Iván
Image Correlation Method for DNA Sequence Alignment
title Image Correlation Method for DNA Sequence Alignment
title_full Image Correlation Method for DNA Sequence Alignment
title_fullStr Image Correlation Method for DNA Sequence Alignment
title_full_unstemmed Image Correlation Method for DNA Sequence Alignment
title_short Image Correlation Method for DNA Sequence Alignment
title_sort image correlation method for dna sequence alignment
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384675/
https://www.ncbi.nlm.nih.gov/pubmed/22761742
http://dx.doi.org/10.1371/journal.pone.0039221
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