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G3 (Bethesda). 2018 Jul 2;8(7):2167-2172. doi: 10.1534/g3.118.200220.

BLAST-XYPlot Viewer: A Tool for Performing BLAST in Whole-Genome Sequenced Bacteria/Archaea and Visualize Whole Results Simultaneously.

Author information

1
Instituto de Ciencias.
2
Facultad de Ciencias de la Computación, Benemérita Universidad Autónoma de Puebla, Puebla, Pue., México CP 72570.
3
Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor., México CP 62210.
4
Instituto de Ciencias luis.fuentes@correo.buap.mx.

Abstract

One of the most commonly used tools to compare protein or DNA sequences against databases is BLAST. We introduce a web tool that allows the performance of BLAST-searches of protein/DNA sequences in whole-genome sequenced bacteria/archaea, and displays a large amount of BLAST-results simultaneously. The circular bacterial replicons are projected as horizontal lines with fixed length of 360, representing the degrees of a circle. A coordinate system is created with length of the replicon along the x-axis and the number of replicon used on the y-axis. When a query sequence matches with a gene/protein of a particular replicon, the BLAST-results are depicted as an "x,y" position in a specially adapted plot. This tool allows the visualization of the results from the whole data to a particular gene/protein in real time with low computational resources.

KEYWORDS:

BLAST-XYPlot viewer; bacterial genomes; large scale BLAST; operon search

PMID:
29789313
PMCID:
PMC6027881
DOI:
10.1534/g3.118.200220
[Indexed for MEDLINE]
Free PMC Article

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