Utilize este identificador para referenciar este registo:
https://hdl.handle.net/1822/14575
Registo completo
Campo DC | Valor | Idioma |
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dc.contributor.author | Deusdado, Sérgio | - |
dc.contributor.author | Carvalho, Paulo | - |
dc.date.accessioned | 2011-11-24T12:34:57Z | - |
dc.date.available | 2011-11-24T12:34:57Z | - |
dc.date.issued | 2009 | - |
dc.identifier.isbn | 9783540858607 | por |
dc.identifier.issn | 1615-3871 | por |
dc.identifier.uri | https://hdl.handle.net/1822/14575 | - |
dc.description | http://www.informatik.uni-trier.de/%7Eley/db/conf/iwpacbb/iwpacbb2008.html | por |
dc.description.abstract | In this paper, we propose SimSearch, an algorithm implementing a new variant of dynamic programming based on distance series for optimal and near-optimal similarity discovery in biological sequences. The initial phase of SimSearch is devoted to fulfil the binary similarity matrices by signalling the distances between occurrences of the same symbol. The scoring scheme is further applied, when analysed the maximal extension of the pattern. Employing bit parallelism to analyse the global similarity matrix’s upper triangle, the new methodology searches the sequence(s) for all the exact and approximate patterns in regular or reverse order. The algorithm accepts parameterization to work with greater seeds for near-optimal results. Performance tests show significant efficiency improvement over traditional optimal methods based on dynamic programming. Comparing the new algorithm’s efficiency against heuristic based methods, equalizing the required sensitivity, the proposed algorithm remains acceptable. | por |
dc.description.sponsorship | This work has been partially supported by PRODEP. | por |
dc.language.iso | eng | por |
dc.publisher | Springer Verlag | por |
dc.rights | openAccess | por |
dc.subject | Similarity discovery | por |
dc.subject | Dynamic programming | por |
dc.subject | Distance series | por |
dc.title | SimSearch: A new variant of dynamic programming based on distance series for optimal and near-optimal similarity discovery in biological sequences | por |
dc.type | conferencePaper | - |
dc.peerreviewed | yes | por |
dc.relation.publisherversion | http://www.springerlink.com/content/t3701n3011675773/ | por |
sdum.publicationstatus | published | por |
sdum.event.title | 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008) | - |
oaire.citationStartPage | 206 | por |
oaire.citationEndPage | 216 | por |
oaire.citationVolume | 49 | por |
dc.identifier.doi | 10.1007/978-3-540-85861-4_25 | por |
dc.subject.wos | Science & Technology | por |
sdum.journal | Advances in Soft Computing | por |
sdum.conferencePublication | 2ND INTERNATIONAL WORKSHOP ON PRACTICAL APPLICATIONS OF COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (IWPACBB 2008) | por |
Aparece nas coleções: | DI/CCTC - Artigos (papers) |
Ficheiros deste registo:
Ficheiro | Descrição | Tamanho | Formato | |
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SimSearch-cr.pdf | SimSearch-cr.pdf (paper) | 356,34 kB | Adobe PDF | Ver/Abrir |