Development of EGene platform for functional annotation and database integration: application and validation on transcript sequences of Eimeria spp. of domestic fowl

• Grant number: 09/12643-8
• Support type: Scholarships in Brazil - Master
• Effective date (Start): March 01, 2010
• Effective date (End): September 30, 2011
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal researcher: Arthur Gruber
• Grantee: Luiz Thibério Lira Diniz Rangel
• Home Institution: Instituto de Ciências Biomédicas (ICB). Universidade de São Paulo (USP). São Paulo , SP, Brazil

Abstract

EGene (Durham et al., Bioinformatics. 21(12): 2812-2813, 2005) is an integrated platform developed by our group for generic pipeline construction. EGene system allows joining a series of processing steps in a single pipeline, with a custom-defined order and composition. Version 2 of the software, not publicly available yet, comprises a wide range of annotation components such as an ORF finder and translation tool, modules for seven gene prediction programs (Genscan, GlimmerM, GlimmerHMM, Twinscan, Phat, ESTscan and SNAP), three tandem repeat finders (TRF, String and MREPs), tRNAscan-SE, cDNA mapping (Sim4 and Exonerate), similarity searching (BLAST), protein motif searching (HMMER/Pfam, RPS-Blast, InterProScan), transmembrane domain (TMHMM) and signal peptide (SignalP) prediction or both (Phobius), GPI anchoring site prediction (DGPI), GO term mapping, and annotation generation in feature table (FT) and GFF3 formats. Another newly developed component automatically constructs a web page where all collected evidences can be easily inspected. In the present project, we intend to increment the scope of applications of the platform, allowing for a full integration with a relational database and to perform functional annotation. We aim to develop new components for orthology analysis using different databases (COG/KOG and eggNOG); protein mapping on KEGG's metabolic pathways; integration of sequence annotation and expression data; integration of automatic annotation and the Generic Genome Browser (GBrowse); integration of EGene with a relational database management system; and development of the computational basis for probabilistic annotation using controlled vocabularies. These new tools will be used to obtain a more refined functional annotation of ORESTES sequencing data produced by our group for three Eimeria species of domestic fowl, and to construct a relational database that will allow performing complex querying and data mining.

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

NOVAES, JENIFFER; RANGEL, LUIZ THIBERIO L. D.; FERRO, MILENE; ABE, RICARDO Y.; MANHA, ALESSANDRA P. S.; DE MELLO, JOANA C. M.; VARUZZA, LEONARDO; DURHAM, ALAN M.; MADEIRA, ALDA MARIA B. N.; GRUBER, ARTHUR. A comparative transcriptome analysis reveals expression profiles conserved across three Eimeria spp. of domestic fowl and associated with multiple developmental stages. International Journal for Parasitology, v. 42, n. 1, p. 39-48, JAN 2012. Web of Science Citations: 18.

Academic Publications

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

RANGEL, Luiz Thibério Lira Diniz. Development of EGene platform for functional annotation and database integration: application and validation on transcript sequences of Eimeria spp. of domestic fowl.. 2012. Master's Dissertation - Universidade de São Paulo (USP). Instituto de Ciências Biomédicas (ICB/SDI) São Paulo.