Título: The Scientific World JournalImportada do Authenticus Pesquisar Publicações da Revista

Vol. 2012 Nº 361496

Páginas: 1-4

ISSN: 2356-6140

Editora: Hindawi

ISI Web of Knowledge - 8 Citações

Scopus - 7 Citações

ID Authenticus: P-002-FEB

DOI: 10.1100/2012/450124

Abstract (EN): The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words-in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

Idioma: Inglês

Tipo (Avaliação Docente): Científica

Contacto: isoares@ipatimup.pt

Nº de páginas: 4