Comparisons of the repeat content of the three Metarhizium spp., using reciprocal blast clustering, revealed surprisingly few common repetitive sequences.
The pipeline is based on all-vs-all BLASTP searches and a reciprocal best BLAST clustering of proteins.
This software first does an all-against-all protein BLAST then clusters these BLAST results based on their scores.
BLAST predicts clusters based on protein sequence, thus the prediction space is limited to sequence related proteins.
Commonly, most researchers use pairwise distance comparisons algorithms, such as BLAST, COG (Clusters of Orthologous Groups), RBH (Reciprocal BLAST Hits), RSD (Reciprocal Smallest Distance Algorithm) and INPARANOID, to determine gene orthology [ 42].
The panorama is derived from the use of two basic tools on the extensive database of amino acid sequences: first, traditional BLAST similarity clusters, and second, our new tool of hierarchical smoothness ordering.
The potential origins of genes identified by GLOOME as acquired along internal branches of the Listeria phylogeny and of "singleton" best BLAST match clusters (genes present in a single Listeria genome) were further investigated through similarity searches (see Materials and Methods).
As expected, genomes reporting a high similarity score in the BLAST matrix cluster on the pan-genome tree, which provides deeper resolution among the C. jejuni genomes than the 16S rRNA tree.
These BLAST and clustering results provide approximate descriptions of gene family size distributions.
