We developed a procedure to identify sequences in three distantly related species (mouse, chicken and zebrafish) that are (1) potential regulatory sequences, (2) orthologous, and (3) not conserved between the species.
Comprehensive assessment of the extent of lateral gene transfer can be made easily by genomic subtraction, a procedure to enrich sequences that are present in one genome but not in another by using biotinylated subtractor DNA to fish out the target DNA by hybrid formation.
Specifically, given the sitewise estimations of the constrained vectors on a window W of size k, we score the window with (13) where (x1 j,…, x j M ) represents the j-th column of aligned bases in W. We also apply the same procedure to neutral sequences to obtain a null distribution of the combined LO scores.
To prevent a potential bias in exon counts through a slight bias in protein sequence lengths in our data, we compared exon counts in C.Prot with Swiss-Prot applying a bootstrap procedure to draw appropriate sequence length distributions from Swiss-Prot.
To achieve a fair and representative presentation for all the genotypes, we applied a multi-step procedure to remove extra sequences from the initial sequences set.
We conclude that the present SBT method is a technically simple and robust procedure to characterize the sequence polymorphisms in exon 2 of DQA1 gene.
BATWING uses a Markov chain Monte Carlo procedure to generate a sequence of genealogic and population trees, with associated model parameter values, consistent with the genetic data observed in a sample of individuals.
If a user discovers a good combination of features to use for priors, it may be desirable to repeat the same procedure to analyze other sequence sets as well.
Specifically, we can either invert the objective function to minimize CC fitness or alter the target CC distribution during the execution of the optimization procedure to design the sequence of the attenuated virus.
The energy balancing procedure leads to sequences presented on the third line of Figure 1.
