TY - JOUR

T1 - Bioinformatics analysis of large-scale viral sequences

T2 - From construction of data sets to annotation of a phylogenetic tree

AU - Munir, Muhammad

PY - 2013/1/1

Y1 - 2013/1/1

N2 - Due to a significant decrease in the cost of DNA sequencing, the number of sequences submitted to the public databases has dramatically increased in recent years. Efficient analysis of these data sets may lead to a significant understanding of the nature of pathogens such as bacteria, viruses, parasites, etc. However, this has raised questions about the efficacy of currently available algorithms for the study of pathogen evolution and construction of phylogenetic trees. While the advanced algorithms and corresponding programs are being developed, it is crucial to optimize the available ones in order to cope with the current need. The protocol presented in this study is optimized using a number of strategies currently being proposed for handling large-scale DNA sequence data sets, and offers a highly efficacious and accurate method for computing phylogenetic trees with limited computer resources. The protocol may take up to 36 h for construction and annotation of a final tree of about 20,000 sequences.

AB - Due to a significant decrease in the cost of DNA sequencing, the number of sequences submitted to the public databases has dramatically increased in recent years. Efficient analysis of these data sets may lead to a significant understanding of the nature of pathogens such as bacteria, viruses, parasites, etc. However, this has raised questions about the efficacy of currently available algorithms for the study of pathogen evolution and construction of phylogenetic trees. While the advanced algorithms and corresponding programs are being developed, it is crucial to optimize the available ones in order to cope with the current need. The protocol presented in this study is optimized using a number of strategies currently being proposed for handling large-scale DNA sequence data sets, and offers a highly efficacious and accurate method for computing phylogenetic trees with limited computer resources. The protocol may take up to 36 h for construction and annotation of a final tree of about 20,000 sequences.

KW - Annotation

KW - DNA dataset

KW - Influenza virus

KW - NS gene

KW - Phylogenetic analysis

KW - Viruses

U2 - 10.4161/viru.23161

DO - 10.4161/viru.23161

M3 - Journal article

AN - SCOPUS:84872874379

VL - 4

SP - 97

EP - 106

JO - Virulence

JF - Virulence

SN - 2150-5594

IS - 1

ER -