INBA   12521
INSTITUTO DE INVESTIGACIONES EN BIOCIENCIAS AGRICOLAS Y AMBIENTALES
Unidad Ejecutora - UE
congresos y reuniones científicas
Título:
The Comparisons of Sequences with the Nucleotide Database (NCBI) and the BLAST tool. What information we can obtain?
Autor/es:
VICTORIA E. FIRMENICH; M. EUGENIA FERNÁNDEZ FEIJÓO ; ESPINOSA MB
Lugar:
Oro Verde
Reunión:
Congreso; 3er. Congreso Argentino de Bioinformática y Biología Computacional; 2012
Institución organizadora:
Asociación Argentina de Bioinformética y Biología Computacional
Resumen:
The Comparisons of Sequences with the Nucleotide Database (NCBI) and the BLAST tool. What information we can obtain? Victoria E. Firmenich, M. Eugenia Fernández Feijóo and María B. Espinosa. Fundación PROSAMA, CONICET. Paysandú 752, C1405ANH. Ciudad Autónoma de Buenos Aires, Argentina. The National Center for Biotechnology Information (NCBI from USA) provides a database "on line" that comprises nucleotide sequences from DNA of genes from microbes, plants, humans and several species used as reference. We conducted sequences analysis using the Basic Local Alignment Search Tool (BLAST). The BLAST tool allows the analysis of a nucleotide sequence obtained from PCR products. The data obtained by sequencing from specific amplifications are analysed by BLAST. We performed studies of AMELX and Vkorc1 using this tool. The genomic DNA used as template was prepared from tissue samples from small mammals species (Akodon azarae, Lagostomus maximus and Mus musculus). In this work we describe this methodology useful to assess nucleotide sequences. After the sequencing of a PCR amplification product, the sequence should be in an archive .doc: …TTAGGTTAGGGCTAAG….a file of letters that represent the four DNA bases is the nucleotide "query" to find coincidences in the official database. Then we choose an organism to pursue the sequence alignment. So far are human, rodents, flowering plants (Arabidopsis thaliana), rice (Oryza sativa) and some others (Pan troglodytes; Danio rerio; Gallus gallus; Drosophila melanogaster, Apis mellifera and Bos taurus) which genome it is known and has been assembled on the NCBI databases for BLAST. The sequence of PCR products for amelogenin gene was obtained from DNA templates of A. azarae and L. maximus. The Amel sequence from Mus musculus and human was used for sequences analysis because those are the closer organisms in which the Amel gene it is described. The BLAST algorithm allowed us to determine that the females from both species shared an intronic sequence with the human Amelogenin gene (M55418); the identities minimal was of 73% in sequences of 200 base pair length. The Vkorc1 sequences obtained for the three exons from wild type mice were compared with the NCBI Reference Sequence: NT_039433.8 corresponding to Mus musculus strain C57BL/6J chromosome 7. The sequences length was from 168 to 311 base pair. A maximum of 6 gaps was found in a 3% of the sequences. The identities between the sequence for the vitamin K epoxide reductase complex from Mus musculus strain C57BL/6J and the wild type was of 87 to 100%. There was no mutation for the Vkorc1 sequence in none of 20 wild rodents analysed. These analyses show that the Vkorc1 exons sequence is well conserved in wild mice from population of Buenos Aires in study. The BLAST allowed us to study the amelogenin gene in species as Akodon azarae and Lagostomus maximus in which Amel was unknown and also the studies of the Vkorc1 from Mus musculus of local wild populations.