New EST trimming procedure applied to SUCEST sequences

Autor(es)

Baudet, Christian ; Dias, Zanoni ; Sagot, MF ; Walter, MEMT

• Tipo de documento: Artigo Científico
• Fonte: Lecture Notes in Computer Science; v. 4643, p. 3-pg., 2007-01-01.

Resumo

In order to improve EST trimming, we proposed a new method consisting of a new set of procedures to detect regions that do Dot belong to the sequenced organism or have low quality or low complexity. Most trimming procedures process ESTs in a pipeline where the output of an step is adopted as the input for the following one. In our method, all artifact detection steps process the raw EST and their results are combined in the last step, which outputs the trimmed sequence. This strategy reduces the occurrence of false negatives and, additionally, has the advantage of producing better artifact composition characterization for the analyzed sequences. We evaluated our method using SUCEST [1] ESTs. Based on the results, we concluded that our method suits projects that want to produce more reliable clusters. (AU)

• Processo FAPESP: 03/07748-9 - Sistema de identificação de polimorfismos
• Beneficiário: Zanoni Dias
• Modalidade de apoio: Auxílio à Pesquisa - Pesquisa Inovativa em Pequenas Empresas - PIPE
• Processo FAPESP: 04/09417-2 - Sistema de identificação de polimorfismos
• Beneficiário: Christian Baudet
• Modalidade de apoio: Bolsas no Brasil - Programa Capacitação - Treinamento Técnico