DR_SEQAN: a PC/Windows-based software to evaluate drug resistance using human immunodeficiency virus type 1 genotypes

BMC Infectious Diseases
César Garriga, Luis Menéndez-Arias

Abstract

Genotypic assays based on DNA sequencing of part or the whole reverse transcriptase (RT)- and protease (PR)-coding regions of the human immunodeficiency virus type 1 (HIV-1) genome have become part of the routine clinical management of HIV-infected individuals. However, the results are difficult to interpret due to complex interactions between mutations found in viral genes. DR_SEQAN is a tool to analyze RT and PR sequences. The program output includes a list containing all of the amino acid changes found in the query sequence in comparison with the sequence of a wild-type HIV-1 strain. Translation of codons containing nucleotide mixtures can result in potential ambiguities or heterogeneities in the amino acid sequence. The program identifies all possible combinations of 2 or 3 amino acids that derive from translation of triplets containing nucleotide mixtures. In addition, when ambiguities affect codons relevant for drug resistance, DR_SEQAN allows the user to select the appropriate mutation to be considered by the program's drug resistance interpretation algorithm. Resistance is predicted using a rule-based algorithm, whose efficiency and accuracy has been tested with a large set of drug susceptibility data. Drug resistance p...Continue Reading

References

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Citations

Jun 10, 2009·The Journal of Antimicrobial Chemotherapy·César GarrigaUNKNOWN Spanish Group for the Study of Antiretroviral Drug Resistance
Jan 1, 2012·JMIR Research Protocols·Yashik Singh, Maurice Mars
Sep 15, 2007·Journal of Medical Virology·César GarrigaUNKNOWN Spanish Group for the Study of Antiretroviral Drug Resistance
Feb 9, 2010·Bioinformatics and Biology Insights·Marcin KierczakJan Komorowski

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Methods Mentioned

BETA
genotyping

Software Mentioned

SEQAN
_ SEQAN ( Drug Resistance SEQuence ANalyzer )
ANRS
Retrogram
RegaInst
DR
Access
BLAST
Windows
Visual Basic

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Antimicrobial Resistance (ASM)

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.

Antimicrobial Resistance

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.