Computational tool for identification to microorganism based in signatures genomics

• Grant number: 13/15174-4
• Support Opportunities: Scholarships in Brazil - Master
• Start date: November 01, 2013
• End date: February 28, 2015
• Field of knowledge: Biological Sciences - Biophysics - Biophysics of Processes and Systems
• Principal Investigator: Jose Luiz Rybarczyk Filho
• Grantee: Tahila Andrighetti
• Host Institution: Instituto de Biociências (IBB). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil

Abstract

The advance of DNA sequence technologies decreased the costs and increased the speed of sequencing, expanding the data generated. However, the development of efficient algoritms to analyse this data doesn't increase. Metagenomics consists of sequencing a lot of microorganisms of an enviroment sample together, without isolating them. It is important, because the many microorganisms can't be cultivated in laboratory. The sequences obtained by metagenomics are little fragments, with less than 700bp. They are usually identified by alignament with entire genomes stored in databases. Although, this methodology of analysis is longstanding and isn't so accurate in the case of little pieces of DNA, because biological factors as horizontal gene transfer and chromossome rearrangements can interfere in the results. An alternative to help this characterization is detection of genome signatures - sequence organization patterns shaped by the selection pressure of the envoiroment on the microorganisms. The genome signatures are species specific, the closer two organisms are in the evolutionary scale, less genome signature are modified. This method doesn't suffer the same inffluences than alignament does, because the signatures are found in entire genome. In this project, sequence organization measures will be used in microorganisms DNA fragments, in order to find genome signatures that can be used to help the recognition of the fragments in a gender level. It can provide a focus between the possibilities to be analysed, simplifying the methodology of sequence characterization. (AU)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

ANDRIGHETTI, Tahila. Ferramenta computacional para identificação de micro-organismos com base em assinaturas genômicas. 2015. Master's Dissertation - Universidade Estadual Paulista (Unesp). Instituto de Biociências. Botucatu Botucatu.