Although the diversity of cluster results was found for p- ompA, the primary proteins structure and function of different patterns were identical predicted by software.
Thus, detailed analysis of the genes re-arranged to code for the scFvs constituting clusters A and B showed that B had a higher diversity than A. This higher diversity of cluster B was also evidenced by the longer branches of the B subtree as compared to A, and this diversity very possibly allowed cluster B to encompass all the best clones.
The prokaryotic diversity indices based on the number of OTUs (operational taxonomic units), Chao1 richness, and Shannon's and Simpson's diversity indices, revealed that the prokaryotic diversity of Cluster I was significantly lower than that of Cluster II (p < 0.001) (Additional file 1: Figure S2, Additional file 2: Table S1).
Clustering of sequences implemented with BLAST and single-linkage clustering produced a wide diversity of cluster sets (Table 2) depending on how we set the minimum hit fraction, which is the set union of the sets of locally aligned sites (hits) reported by BLAST.
The diversity of cluster B was quickly appreciated from the branch lengths of the corresponding phylogenetic sub-tree, as opposed to the sub-tree representing cluster A. In the future, these phylogenetic trees could well be a useful guide for the testing of clones eluted from immune libraries, all the more if more numerous sequences are to be analyzed.
The methanogen clones were of low diversity and clustered in three sub-groups.
This study revealed the diversity of TOMM clusters as well as the phylogenetic distribution of clusters in both bacteria and archaea.
In an attempt to improve ShoRAH's performance under conditions of sub-optimal diversity or clustered systematic errors, we applied a statistical test of strand bias to the raw SNV calls.
The diversity of the clusters (i.e. the number of unique sequences within a cluster) is the highest in the first selection rounds.
The diversity of the six clustered Sp185/333 genes were compared to 121 unique Sp185/333 genes collected randomly from three individual sea urchins for which the relative genomic organization was unknown [ 15].
