In particular, we show some cases where sequencing by hybridization using reference sequences will not be feasible due to the amount of variability in the target sequence.
A total of 591 HCV sequences obtained from São Paulo State were successfully amplified, sequenced and typed by phylogenetic analysis using reference sequences obtained from the Los Alamos HCV database.
bOrganism of the used reference sequence.
Preliminary analysis indicated good coverage of the polymerase region of the ARCoV.2 reference sequence by the reads (quality index >40) by using reference assembly against CoV complete genomes.
Orthologous proteins were identified by BLASTP using reference proteins from previously sequenced N. meningitidis and N. gonorrhoeae genomes where possible.
However, note that our focus is on re-sequencing studies, and if we have even a crude idea on the genomic coordinates of the BACs, we can approximate that missing information by using the reference sequence.
The genes within the cps loci that encoded proteins with the same homology group were assigned the same name, exceptions being those genes found in Region A. BLASTp (http://blast.ncbi.nlm.nih.gov/Blast.cgi PAGE=Proteins) searches were done by using a reference sequence database with default settings.
The tropism characteristics of each U3 sequence was determined by comparison analysis using the reference sequences (direct repeats, unique region, and 190 bp insertion) first reported by Tomonaga et al. [ 30].
Each step was carried out with negative controls.> All assembled sequences were submitted to the Los Alamos National Laboratory HIV Sequence Database (http://www.hiv.lanl.gov/content/index) to determine HIV genotype, which were further confirmed by phylogenetic analysis using standard reference sequences representing subtypes A D, F H, J, K, CRF01_AE, CRF07_BC, and CRF08_BC (www.hiv.lanl.gov).hiv.lanl.gov
