Exact(5)
We used the repeats patterns to identify additional, smaller and/or degenerate repeat clusters in the 4 CRISPR-associated genomic regions (i.e. cysD-cysJ; cysJ-ygcF; clpS-tRNASer and tRNASer-infA) in the 51 Escherichia/Salmonella complete genomes with Fuzznuc (http://bioweb2.pasteur.fr/docs/EMBOSS/fuzznuc.html).
On the other hand, most of the complex repeats usually have sophisticated patterns of repeat units with variable lengths ranging from 10 to >100 residues, and these complex repeats patterns are frequently recognized as repeated protein domains [ 3].
Since SSRs are prone to slip-strand mispairing, which is demonstrated as a primary source of microsatellite mutational expansion [ 45], we applied a length threshold greater than 10 bp for mono-, 4 bp for di- and tri- and 3 minimum repetitive units for tetra-, penta- and hexa-nucleotide repeats patterns.
In an attempt to further characterize the candidate genes, we followed an in-depth bioinformatic analysis which was aimed at revising the existing annotation, as well as determining the cellular localization and the presence of secretion signals, and protein repeats patterns.
However, this pathogen differs from the closely related dassie bacillus in its mycobacterial interspersed repetitive unit variable number tandem repeats patterns (Table 2) by being a unique RD5das variant and by containing 21 copies of the IS 6110 insertion element (compared with 10 15 copies in the dassie bacillus) (2 ).
Similar(55)
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