jyguard55 Goto Github PK
Name: Jean Guard
Type: User
Company: US Department of Agriculture
Location: Athens, GA
Name: Jean Guard
Type: User
Company: US Department of Agriculture
Location: Athens, GA
The dkgB-linked intergenic sequence ribotype (ISR) region of Salmonella enterica subspecies I can be used to screen for serotype. The ISR database is reviewed by BLAST in comparison to NCBI complete and draft genomes, which respectively had approximately 662 and 7,900 genomes as of end of March 2018. It was developed by triangulation with Kauffman-White-LeMinor antisera based typing and DNA microarray hybridization that is AOAC approved in Europe. It is being reviewed in comparison to MLST data. This is a screening assay meant to be used for applied testing programs. Data requirements are minimized. USDA makes this available as a democratized assay having applied value for protecting the safety of the food supply, and thus should be made widely available. It will be updated periodically.
The dkgB-linked intergenic sequence region (ISR) can be used to match sequence to text in the database. Only 100% perfect similarity and length matches count towards identifying serotype. The qualifier "also" in the filename indicates data that are emerging from the NCBI BLAST database but lack the numbers to make a final determination based on the weight of evidence. The qualifier "false" indicates that the ISR specific to the serotype occurs in another serotype, but not linked to the dkgB gene. The dkgB gene should be within 500bp of the 5S rRNA gene in the middle of the ISR sequence or linkage does not exist.
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