GenSeed-HMM: development of a platform for sequence reconstruction and application on next-generation sequencing data.

Author(s)

André Luiz de Oliveira

• Document type: Master's Dissertation
• Press: São Paulo.
• Institution: Universidade de São Paulo (USP). Instituto de Ciências Biomédicas (ICB/SDI)
• Defense date: 2012-08-14

Examining board members

Arthur Gruber; Paulo Sérgio Lopes de Oliveira; Gerhard Wunderlich

• Advisor: Arthur Gruber

Abstract

The program GenSeed, previously described by our group, implements a seed-driven progressive assembly method for target-specific assembly of DNA sequences, starting from short DNA or protein seed sequences. The program can be applied for the reconstruction of genomic fragments, extrachromosomal genomes, and cDNAs, but is not adequate for sequence reconstruction using seed sequences and databases derived from heterologous samples. The present work aimed at developing GenSeed-HMM, a new version of GenSeed program that can use profile HMMs as seeds for the reconstruction of specific sequences, and incorporates the ability to work with data generated by the new sequencing platforms, including short reads. This work reports the implementation of GenSeed-HMM program and its validation using real life data produced by different next-generation sequencing platforms, and originated from prokaryotic, eukaryotic and metagenomic samples. (AU)

• FAPESP's process: 10/04609-1 - GenSeed-HMM: development of a platform for sequence reconstruction and application on novel virus discovery
• Grantee: André Luiz de Oliveira
• Support Opportunities: Scholarships in Brazil - Master