Statistical method of context evaluation for biological sequence similarity

Within this paper we are proposing and testing a new strategy for detection and measurement of similarity between sequences of proteins. Our approach has its roots in computational linguistics and the related techniques for quantifying and comparing content in strings of characters. The pairwise com...

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Detalles Bibliográficos
Autores principales: Lyroudia, Kleoniki, Bogan-Marta, Alina, Pitas, Ioannis
Formato: Objeto de conferencia
Lenguaje:Inglés
Publicado: 2006
Materias:
Ciencias Informáticas
Similarity measures
Linguistics
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/23873
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
id I19-R120-10915-23873
record_format dspace
institution Universidad Nacional de La Plata
institution_str I-19
repository_str R-120
collection SEDICI (UNLP)
language Inglés
topic Ciencias Informáticas
Similarity measures
Linguistics
spellingShingle Ciencias Informáticas
Similarity measures
Linguistics
Lyroudia, Kleoniki
Bogan-Marta, Alina
Pitas, Ioannis
Statistical method of context evaluation for biological sequence similarity
topic_facet Ciencias Informáticas
Similarity measures
Linguistics
description Within this paper we are proposing and testing a new strategy for detection and measurement of similarity between sequences of proteins. Our approach has its roots in computational linguistics and the related techniques for quantifying and comparing content in strings of characters. The pairwise comparison of proteins relies on the content regularities expected to uniquely characterize each sequence. These regularities are captured by n-gram based modelling techniques and exploited by cross-entropy related measures. In this new attempt to incorporate theoretical ideas from computational linguistics into the field of bioinformatics, we experimented using two implementations having always as ultimate goal the development of practical, computationally efficient algorithms for expressing protein similarity. The experimental analysis reported herein provides evidence for the usefulness of the proposed approach and motivates the further development of linguistics-related tools as a means of analysing biological sequences.
format Objeto de conferencia
Objeto de conferencia
author Lyroudia, Kleoniki
Bogan-Marta, Alina
Pitas, Ioannis
author_facet Lyroudia, Kleoniki
Bogan-Marta, Alina
Pitas, Ioannis
author_sort Lyroudia, Kleoniki
title Statistical method of context evaluation for biological sequence similarity
title_short Statistical method of context evaluation for biological sequence similarity
title_full Statistical method of context evaluation for biological sequence similarity
title_fullStr Statistical method of context evaluation for biological sequence similarity
title_full_unstemmed Statistical method of context evaluation for biological sequence similarity
title_sort statistical method of context evaluation for biological sequence similarity
publishDate 2006
url http://sedici.unlp.edu.ar/handle/10915/23873
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bdutipo_str Repositorios
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