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English Information

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Authors
# Name
1 Pedro M. Barcelos(pbarcelos@inf.puc-rio.br)
2 Marcos Catanho(mcatanho@fiocruz.br)
3 Antônio B. de Miranda(amiranda@fiocruz.br)
4 Edward Haeusler(hermann@inf.puc-rio.br)
5 Sérgio Lifschitz(sergio@inf.puc-rio.br)

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Reference
# Reference
1 Uniprot: the universal protein knowledgebase in 2025. Nucleic acids research, 53(D1):D609–D617.
2 Abrahim, M., Machado, E., Alvarez-Valín, F., de Miranda, A. B., and Catanho, M. (2022). Uncovering pseudogenes and intergenic protein-coding sequences in tritryps’ genomes. Genome Biology and Evolution, 14(10):evac142
3 Blattner, F. R., Plunkett III, G., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado- Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., et al. (1997). The complete genome sequence of escherichia coli k-12. science, 277(5331):1453–1462
4 Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T. L. (2009). Blast+: architecture and applications. BMC bioinformatics, 10(1):421.
5 Pearson, W. R. (2000). Flexible sequence similarity searching with the fasta3 program package. In Bioinformatics methods and protocols, pages 185–219. Springer.
6 Rost, B. (1999). Twilight zone of protein sequence alignments. Protein engineering, 12(2):85–94.
7 Smith, T. F., Waterman, M. S., et al. (1981). Identification of common molecular subse- quences. Journal of molecular biology, 147(1):195–197.
8 Xiao, J., Sekhwal, M. K., Li, P., Ragupathy, R., Cloutier, S., Wang, X., and You, F. M. (2016). Pseudogenes and their genome-wide prediction in plants. International Jour- nal of Molecular Sciences, 17(12):1991.
9 Zheng, D., Frankish, A., Baertsch, R., Kapranov, P., Reymond, A., Choo, S. W., Lu, Y., Denoeud, F., Antonarakis, S. E., Snyder, M., et al. (2007). Pseudogenes in the en- code regions: consensus annotation, analysis of transcription, and evolution. Genome research, 17(6):839–851.