Blast-emm & emm databases

 

Procedure:

• Step A. Use at least the first 240 bases of sequence (edited for accuracy) obtained with primer 1 or emmseq2 (see emm typing protocol page ) to query the type-specific DNA sequence database. Most queries will obtain an exact 180/180 match that can be assigned to the sequence (e.g., emm4.4 is equivalent to type emm4, subtype emm4.4).
  Step B. This database of trimmed 180 base entries corresponds to the first 50 residues of the mature M protein and the adjacent 10 C terminal residues of the signal sequence. The subtype has been correctly identified for subtype designation if a perfect 180/180 match is obtained from the type-specific BLAST.
• If you do not obtain a subtype assignment in step A, please submit the sequence using the form at https://wwwn.cdc.gov/StrepLab/submission.aspx. After verification, CDC Streptococcus Laboratory will assign the sequence a new type and/or subtype and add it to the emm sequence database. Strain, epidemiologic, and clinical information will be included if provided and the database will acknowledge you and your institution for the contribution.

The M type-specific sequence databases can be downloaded from
https://ftp.cdc.gov/pub/infectious_diseases/biotech/tsemm/ (for DNA).
https://ftp.cdc.gov/pub/infectious_diseases/biotech/tstransl/ (for translations).

Note also that the untrimmed peptide and DNA databases can be downloaded from:
https://ftp.cdc.gov/pub/infectious_diseases/biotech/emmsequ/ (for DNA).
https://ftp.cdc.gov/pub/infectious_diseases/biotech/emmtransl/ (for translations).

If you have questions please contact us at GASemmtyping@cdc.gov.

If you wish to submit more than one request, use the ' back ' button on the web browser tool bar after you are notified that your first request has been received. Then you may scroll to change fields and not have to re-type all fields. Results will be sent to your e-mail address from sender ' nobody ' or ' anonymous '.

 

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