After submitting your sequence (either 16S rRNA stretch or complementary oligomer sequence) the server will align the region with 16S rRNA and output the properties of that sequence (or complementary if you input the oligomer sequence). We use a dynamic programming algorithm in order to align such short sequences (between 5 and 20 nucleotides long) with the sequence of the E. coli 16S rRNA. Regions in 16S rRNA that your sequence aligns to are going to be characterized with
described parameters (see About).
With 16S rRNA you can both align the possible oligomer sequence (set the Reverse Transcribe to Yes) or the possible target region (leave the Reverse Transcribe at No).
You can view the alignment parameters via clicking on Parameters. After the output is generated you can view the detailed properties of the targeted region by clicking on one of the listed coordinates.
references:
The Ribosomal Mutation Database YASSIN refers to the 16S rRNA mutation database:
Yassin, Aymen, Kurt Fredrick, and Alexander S Mankin, Deleterious Mutations in Small Subunit Ribosomal RNA Identify Functional Sites and Potential Targets for Antibiotics., Proceedings of the National Academy of Sciences of the United States of America, 102 (2005), 16620-25
Yassin, Aymen, and Alexander S. Mankin, Potential New Antibiotic Sites in the Ribosome Revealed by Deleterious Mutations in RNA of the Large Ribosomal Subunit, Journal of Biological Chemistry, 282 (2007), 24329-42
⇨ Parameters
The Ribosomal Mutation Database YASSIN refers to the 16S rRNA mutation database:
Yassin, Aymen, Kurt Fredrick, and Alexander S Mankin, Deleterious Mutations in Small Subunit Ribosomal RNA Identify Functional Sites and Potential Targets for Antibiotics., Proceedings of the National Academy of Sciences of the United States of America, 102 (2005), 16620-25
Yassin, Aymen, and Alexander S. Mankin, Potential New Antibiotic Sites in the Ribosome Revealed by Deleterious Mutations in RNA of the Large Ribosomal Subunit, Journal of Biological Chemistry, 282 (2007), 24329-42