Using a matrix analysis that did not rely on global sequence alignment, we searched for short, nearly identical sequences (30 bp of 70% sequence identity) surrounding Agrp in pairwise comparisons of vertebrate species.
We applied a simple filter to remove nearly identical sequences, clustered with blastclust at 40% identity and removed singleton clusters to obtain 105,547 homolog clusters.
In the first step, the clustering threshold, which is the similarity cut-off within a cluster, was set at a sequence identity ≥90% in order to eliminate redundant (nearly identical) sequences.
Low disease Veillonella have nearly identical sequences typical of a single species (> 97%16SS rRNA gene sequence identity), as represented in Figure 4.
Although DGATs from a wide range of organisms have nearly identical sequences, there is little structural information available for these enzymes.
Aside from the facts that pericentromeres and mat contain nearly identical sequences and bind the same set of proteins4,5, a dcr1− swi6− double mutant fails to initiate and maintain mat silencing8.
The human genome contains abundant nearly identical sequences (e.g. pseudogenes) to mRNA transcript sequences, which amplify when performing RT-PCR on samples with even trace amounts of genomic DNA.
The first was the unexpected presence of identical or nearly identical sequences in some of the BAL samples.
These nearly identical sequences might lead to inflated estimates of functional genetic elements or introduce an artificial shift in taxonomic profiles, unless they are filtered from the dataset.
The presence, for both loci, of large clades of nearly identical sequences from cattle isolates suggests a rapid spread among cattle.
Another factor that could contribute to a decrease in overall BM diversity is the presence of two or more identical or nearly identical sequences within individuals' BM.
