To find potential synteny blocks between the M. brunnea genome and the genomes of B. cinerea and S. sclerotiorum, we used the BLAST analysis (BLASTN, with the alignment length of longer than 60 bp and over 75% identity) of the M. brunnea genome against the genomes of B. cinerea and S. sclerotiorum.
The comparative analysis of 16S rRNA sequence of M. indicus pranii (MIP) by using the BLAST sequence analysis at NCBI showed a similarity of more than 99% with other closely related mycobacteria: M. intracellulare, M. arosiense, M. chimaera, M. seoulense, M. avium subspecies hominissuis, M. avium subspecies paratuberculosis, and M. bohemicum.
In the five mouse datasets, 12,778 HC pairs out of approximately 20,000 used for the BLAST analysis were commonly seen in two or more datasets.
Of the 65 total differences, 37 were found to be SNPs (including 27 sites annotated with ambiguity codes in the GenBank sequence used in the BLAST analysis because that individual was heterozygous at those positions).
The sequence analysis (using the BLAST database of the National Center for Biotechnology Information; [http://www.ncbi.nlm.nih.gov]) showed that strain Sm777 matched 99.5% with 16S rDNA of the S. maltophilia LMG 958T (accession n° DQ469587).
Genome coverage analysis using the Blast algorithm indicated that approximately 90% of genome is shared among the five SDSE strains (supplementary table S3, Supplementary Material online).
The criterion for sequence match, expected value E = 1e−30, was used to perform the blast analysis.
The criterion for sequence match, expected value E = 1e-30, was used to perform the blast analysis.
A comparative sequence analysis using the BLAST-X algorithm suggests similarity to genes of the esterase-lipase family, in particular to genes of Tribolium castaneum and Apis mellifera that are similar to an uncharacterised Drosophila gene ortholog.
