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Saeedeh Ghiasvand

Saeedeh Ghiasvand

Academic rank: Assistant Professor
ORCID:
Education: PhD.
ScopusId:
HIndex:
Faculty: science
Address:
Phone: 09120929781

Research

Title
Identification of the best algorithm for horizontal genes study on antibiotic resistance genes in Escherichia coli
Type
Presentation
Keywords
horizontal genes, antibiotic resistance genes, Escherichia coli, Bioinformatics
Year
2018
Researchers Saeedeh Ghiasvand

Abstract

Horizontal gene transfer (HGT) is the most important factor in order to make evolution in prokaryotes, main environmental adaptation, and same bacteria resistant mechanism. There are many algorithms from tools for identification of horizontally transferred genes and genomic islands on the bacteria. The SeqWord Genome Browser (SWGB) based on Oligo-nucleotide usage (OU) statistics to visualize which investigated for sequences of different lengths are comparable provided. The 40 genes sequences, related to antibiotic resistance genes in Escherichia coli in the NCBI database, were analyzed by the following statistical parameters: D for distance two same type, PS for distance two direct and reverse strands of the same DNA sequence; RV and GRV usage variances normalized locally and globally, and reduced to the OU variance expected for a randomly generated sequence, GC-content (GC) and GC-skew (GCS) in DNA. We fund that n1_4mer: RV for the X axis, n1_4mer: GRV for the Y axis and n0_4mer: D for the Z axis is the best program in order to antibiotic resistance genes transfer illusion in the SWGB software. On the dot-plot diagram, each gene is represented by a dot with X and Y parameters chosen from X and Y drop-down lists, respectively