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The sequences were analyzed for gene conversion by using the Geneconv program with default parameters [ 41].
Aligned allergen gene CDS were used for analysis of gene conversion using the GENECONV software as described in Sawyer (1989).
Each marker was tested for recombination events using the GENECONV [ 49], MaxChi [ 50], and RDP methods [ 51].
To further establish whether gene conversion has occurred, and identify the boundaries for each species, we made an analysis using the Geneconv program [ 12] (Table 1).
Using the GENECONV program, we also detected that tracts of gene conversions between L and M opsin genes occurred mostly within the intron regions.
To determine whether gene conversion played a similar prominent role in the evolution of vertebrate Ugt1 clusters, we used the Geneconv program [ 41] to search for gene conversion events among Ugt1 variable exons.
Sequence exchange was evaluated using the programs RDP, Geneconv [ 79] and Bootscan [ 80], implemented in RDP version 3.34 [ 44] with defaults parameters except for the Bootscan method where 200 bootstraps and a 90% cut-off value were used.
Using the program GENECONV [ 25] a series of inter- and intra paralog conversion events are evident.
Putative genetic recombination events occurring in Xanthomonas genomes were examined by using the software geneconv [ 86] and PhiPack [ 87].
We searched for evidence of ongoing gene conversion between copies of ta-TRIMs in each species using the program GENECONV (Sawyer 1989, 1999).
Alignments of ta-TRIMs for each taeniid species were analyzed using the program GENECONV (Sawyer 1999), which looks for statistically significant tracts of identity between two sequences, given their overall divergence.
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