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| Indexado |
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| DOI | 10.1109/DCC50243.2021.00027 | ||||
| Año | 2021 | ||||
| Tipo | proceedings paper |
Citas Totales
Autores Afiliación Chile
Instituciones Chile
% Participación
Internacional
Autores
Afiliación Extranjera
Instituciones
Extranjeras
Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this case, which Rossi et al. recently implemented, but it uses two passes over the patterns and buffers a pointer for each character during the first pass. In this paper, we simplify their solution and make it streaming, at the cost of slowing it down slightly. This means that, first, we can compute the matching statistics of several long patterns (such as whole human chromosomes) in parallel while still using a reasonable amount of RAM; second, we can compute matching statistics online with low latency and thus quickly recognize when a pattern becomes incompressible relative to the database. Our code is available at https ://github com/koeppl/phoni.
| Ord. | Autor | Género | Institución - País |
|---|---|---|---|
| 1 | Boucher, Christina | Mujer |
UNIV FLORIDA - Estados Unidos
University of Florida - Estados Unidos |
| 2 | Gagie, Travis | Hombre |
Dalhousie Univ - Canadá
Dalhousie University - Canadá |
| 3 | Tomohiro, I | - |
Kyutech - Japón
Kyushu Institute of Technology - Japón |
| 4 | Koeppl, Dominik | Hombre |
TMDU - Japón
Tokyo Medical and Dental University - Japón |
| 5 | Langmead, Ben | - |
Johns Hopkins Univ - Estados Unidos
Johns Hopkins University - Estados Unidos |
| 6 | Manzini, Giovanni | Hombre |
Univ Piemonte Orientale - Italia
Università degli Studi del Piemonte Orientale "Amedeo Avogadro" - Italia Università degli Studi del Piemonte Orientale “Amedeo Avogadro” - Italia |
| 7 | NAVARRO-BADINO, GONZALO | Hombre |
Universidad de Chile - Chile
|
| 8 | PACHECO-VALLES, ALEJANDRO | Hombre |
Universidad de Chile - Chile
|
| 9 | Rossi, Massimiliano | Hombre |
UNIV FLORIDA - Estados Unidos
University of Florida - Estados Unidos |
| 10 | Bilgin, A | - | |
| 11 | Marcellin, MW | - | |
| 12 | SerraSagrista, J | - | |
| 13 | Storer, JA | - |
| Fuente |
|---|
| National Science Foundation |
| Fondo Nacional de Desarrollo Científico y Tecnológico |
| National Institutes of Health |
| JSPS KAKENHI |
| Japan Society for the Promotion of Science |
| Natural Sciences and Engineering Research Council of Canada |
| National Institute of Allergy and Infectious Diseases |
| NSERC |
| Basal Funds |
| NIH NIAID |
| ANID |
| ANID, Chile |
| NSF IIS |
| FONDECYT, ANID, Chile |
| National Science Foundation NSF IIBR |
| National Institutes of Health (NIH) NIAID |
| NSF SCH: INT |
| Agradecimiento |
|---|
| MR, TG, BL and CB are funded National Science Foundation NSF IIBR (Grant No. 2029552) and National Institutes of Health (NIH) NIAID (Grant No. HG011392). CB is funded by NSF SCH: INT: (Grant No. 2013998). MR and CB are funded by NSF IIS (Grant No. 1618814) and NIH NIAID (Grant No. R01AI141810). TG is funded by NSERC Discovery Grant RGPIN-071852020. DK is funded by JSPS KAKENHI Grant JP18F18120. GN funded by Basal Funds FB0001 and Fondecyt Grant 1-200038, ANID, Chile. AP funded by Basal Funds FB0001 and Doctoral Scholarship grant 21180760, ANID, Chile. |
| MR, TG, BL and CB are funded National Science Foundation NSF IIBR (Grant No. 2029552) and National Institutes of Health (NIH) NIAID (Grant No. HG011392). CB is funded by NSF SCH: INT: (Grant No. 2013998). MR and CB are funded by NSF IIS (Grant No. 1618814) and NIH NIAID (Grant No. R01AI141810). TG is funded by NSERC Discovery Grant RGPIN-07185-2020. DK is funded by JSPS KAKENHI Grant JP18F18120. GN funded by Basal Funds FB0001 and Fondecyt Grant 1-200038, ANID, Chile. AP funded by Basal Funds FB0001 and Doctoral Scholarship grant 21180760, ANID, Chile. |