Sequence Quality Analysis Tool for HIV Type 1 Protease and Reverse Transcriptase
| Autor: | Joseph W. Hogan, Zhijin Wu, Neil Parkin, Allison DeLong, Rami Kantor, Diane E Bennett, Mingham Wu |
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| Rok vydání: | 2012 |
| Předmět: |
Epidemiology
Sequence analysis medicine.medical_treatment Immunology Human immunodeficiency virus (HIV) HIV Infections Biology medicine.disease_cause HIV Protease Virology Drug Resistance Viral medicine Phylogeny Sequence (medicine) chemistry.chemical_classification Protease Base Sequence Sequence Analysis DNA HIV Reverse Transcriptase Reverse transcriptase Stop codon Amino acid Infectious Diseases chemistry HIV-1 Nucleic acid Peptide Hydrolases |
| Zdroj: | AIDS Research and Human Retroviruses. 28:894-901 |
| ISSN: | 1931-8405 0889-2229 |
| DOI: | 10.1089/aid.2011.0120 |
| Popis: | Access to antiretroviral therapy is increasing globally and drug resistance evolution is anticipated. Currently, protease (PR) and reverse transcriptase (RT) sequence generation is increasing, including the use of in-house sequencing assays, and quality assessment prior to sequence analysis is essential. We created a computational HIV PR/RT Sequence Quality Analysis Tool (SQUAT) that runs in the R statistical environment. Sequence quality thresholds are calculated from a large dataset (46,802 PR and 44,432 RT sequences) from the published literature (http://hivdb.Stanford.edu). Nucleic acid sequences are read into SQUAT, identified, aligned, and translated. Nucleic acid sequences are flagged if with >five 1–2-base insertions; >one 3-base insertion; >one deletion; >six PR or >18 RT ambiguous bases; >three consecutive PR or >four RT nucleic acid mutations; >zero stop codons; >three PR or >six RT ambiguous amino acids; >three consecutive PR or >four RT amino acid mutations; >zero unique amino acids; or 15% genetic distance from another submitted sequence. Thresholds are user modifiable. SQUAT output includes a summary report with detailed comments for troubleshooting of flagged sequences, histograms of pairwise genetic distances, neighbor joining phylogenetic trees, and aligned nucleic and amino acid sequences. SQUAT is a stand-alone, free, web-independent tool to ensure use of high-quality HIV PR/RT sequences in interpretation and reporting of drug resistance, while increasing awareness and expertise and facilitating troubleshooting of potentially problematic sequences. |
| Databáze: | OpenAIRE |
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