Automatic annotation

PANNOTATOR: an automated tool for annotation of pan-genomes

A. R. Santos, Barbosa, E., Fiaux, K., Zurita-Turk, M., Chaitankar, V., Kamapantula, B., Abdelzaher, A., Ghosh, P., Tiwari, S., Barve, N., Jain, N., Barh, D., Silva, A., Miyoshi, A., and Azevedo, V., PANNOTATOR: an automated tool for annotation of pan-genomes, vol. 12, pp. 2982-2989, 2013.

Due to next-generation sequence technologies, sequencing of bacterial genomes is no longer one of the main bottlenecks in bacterial research and the number of new genomes deposited in public databases continues to increase at an accelerating rate. Among these new genomes, several belong to the same species and were generated for pan-genomic studies. A pan-genomic study allows investigation of strain phenotypic differences based on genotypic differences.

Bioinformatics of the Paracoccidioides brasiliensis EST Project

M. M. Brígido, Walter, M. Emilia M. T., Walter, M. Emilia M. T., Oliveira, A. G., Inoue, M. K., Anjos, D. S., Sandes, E. F. O., Gondim, J. J., Carvalho, M. José de A., Almeida, Jr., N. F., and Felipe, M. Sueli Soar, Bioinformatics of the Paracoccidioides brasiliensis EST Project, vol. 4, pp. 203-215, 2005.

Paracoccidioides brasiliensis is the etiological agent of paracoccidioidomycosis, an endemic mycosis of Latin America. This fungus presents a dimorphic character; it grows as a mycelium at room temperature, but it is isolated as yeast from infected individuals. It is believed that the transition from mycelium to yeast is important for the infective process.

A new set of bioinformatics tools for genome projects

L. G. P. Almeida, Paixão, R., Souza, R. C., da Costa, G. C., de Almeida, D. F., and de Vasconcelos, A. T. R., A new set of bioinformatics tools for genome projects, vol. 3, pp. 26-52, 2004.

A new tool called System for Automated Bacterial Integrated Annotation - SABIA (SABIÁ being a very well-known bird in Brazil) was developed for the assembly and annotation of bacterial genomes. This system performs automatic tasks of assembly analysis, ORFs identification/analysis, and extragenic region analyses. Genome assembly and contig automatic annotation data are also available in the same working environment.

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