title: Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase.
abstract: 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 <0.5% 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.
authors.affiliation: Center for Statistical Sciences, Brown University, Providence, Rhode Island 02906, USA.
authors.forename: Allison K
authors.initials: AK
authors.lastname: Delong
authors.forename: Mingham
authors.initials: M
authors.lastname: Wu
authors.forename: Diane
authors.initials: D
authors.lastname: Bennett
authors.forename: Neil
authors.initials: N
authors.lastname: Parkin
authors.forename: Zhijin
authors.initials: Z
authors.lastname: Wu
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Hogan
authors.forename: Rami
authors.initials: R
authors.lastname: Kantor
mesh_terms: D001483:Base Sequence; D024882:Drug Resistance, Viral / Q000235:genetics*; D015658:HIV Infections / Q000821:virology*; D016333:HIV Protease / Q000235:genetics*; D054303:HIV Reverse Transcriptase / Q000737:chemistry / Q000235:genetics*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D010447:Peptide Hydrolases / Q000737:chemistry; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D054303:HIV Reverse Transcriptase; D010447:Peptide Hydrolases; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1