Colección SciELO Chile

Departamento Gestión de Conocimiento, Monitoreo y Prospección
Consultas o comentarios: productividad@anid.cl
Búsqueda Publicación
Búsqueda por Tema Título, Abstract y Keywords



Image Correlation Method for DNA Sequence Alignment
Indexado
WoS WOS:000305825800024
Scopus SCOPUS_ID:84862980508
DOI 10.1371/JOURNAL.PONE.0039221
Año 2012
Tipo artículo de investigación

Citas Totales

Autores Afiliación Chile

Instituciones Chile

% Participación
Internacional

Autores
Afiliación Extranjera

Instituciones
Extranjeras


Abstract



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.

Revista



Revista ISSN
P Lo S One 1932-6203

Métricas Externas



PlumX Altmetric Dimensions

Muestra métricas de impacto externas asociadas a la publicación. Para mayor detalle:

Disciplinas de Investigación



WOS
Biology
Multidisciplinary Sciences
Scopus
Sin Disciplinas
SciELO
Sin Disciplinas

Muestra la distribución de disciplinas para esta publicación.

Publicaciones WoS (Ediciones: ISSHP, ISTP, AHCI, SSCI, SCI), Scopus, SciELO Chile.

Colaboración Institucional



Muestra la distribución de colaboración, tanto nacional como extranjera, generada en esta publicación.


Autores - Afiliación



Ord. Autor Género Institución - País
1 CURILEM-SALDIAS, GLORIA MILLARAY Mujer Universidad de La Frontera - Chile
Centro de Genomica Nutricional Agroacuicola - Chile
Seremia de Salud Región de La Araucanía - Chile
Museo Regional de la Araucanía - Chile
2 Villarroel Sassarini, Felipe Hombre Universidad de La Frontera - Chile
3 MUNOZ-TORRES, CARLOS ALBERTO Hombre Universidad de La Frontera - Chile
Centro de Genomica Nutricional Agroacuicola - Chile
Seremia de Salud Región de La Araucanía - Chile
Museo Regional de la Araucanía - Chile
4 VARGAS-VASQUEZ, ASTICIO JUNIOR - Universidad de La Frontera - Chile
5 MAUREIRA-BUTLER, IVAN JORGE Hombre Centro de Genomica Nutricional Agroacuicola - Chile
Seremia de Salud Región de La Araucanía - Chile
Museo Regional de la Araucanía - Chile

Muestra la afiliación y género (detectado) para los co-autores de la publicación.

Financiamiento



Fuente
Research Direction of the La Frontera University
Genomic and Bioinformatics Unit of the Agriaquaculture Nutritional Genomic Center (CGNA), CONICYT-Regional, GORE La Araucania

Muestra la fuente de financiamiento declarada en la publicación.

Agradecimientos



Agradecimiento
The Research Direction of the La Frontera University and the Genomic and Bioinformatics Unit of the Agriaquaculture Nutritional Genomic Center (CGNA), CONICYT-Regional, GORE La Araucania, R10C1001 financed the work presented in the paper. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Muestra la fuente de financiamiento declarada en la publicación.