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The capacity to identify linked mutations could be important for understanding the persistence [20] and clinical impact of mutant variants.
The HIV codon covariation analysis can be used to identify linked pathways of immune escape, as well as putative secondary and/or compensatory mutations associated with a primary escape site.
For most pairs (42/49) whose sequences did not show clear evidence of linkage by env or gag consensus sequencing, multiple single molecule (SM) C2-V3-C3 env sequences were obtained following endpoint dilution of cDNA from the HIV-1 infected partner's plasma to identify linked variants present at lower frequency.
We employed exon capture with BSA to identify linked scaffolds.
The whole genome including multiple unassigned scaffolds can be easily scanned to identify linked regions.
To identify linked SNPs, variant call format (vcf) files were downloaded from the 1000 Genomes project (phase 1) and converted to PLINK input files (EUR subpopulation).
Similar(46)
The first step identified linked markers by a two-point analysis with the two-point option.
Yet in these four teleosts, a second Nanos1 gene was identified, linked to Loxl3, Dok1, Np620159.2, Sema4f and Ttc31.
It also shows that the low coverage of sequencing identifies linked regions across several cM in the F4.
When mapping segmental duplications, a duplication block was identified linking LOC_Os03g21040 (chromosome 3) with LOC_Os07g48460 (chromosome 7).
New co-chaperones are also being identified linking the heat shock proteins to previously unknown functions.
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