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Streptococcus pyogenes emm sequence database

Home: CDC Streptococcus Lab > Blast-emm and download emm databases

Blast-emm


Streptococci Group A Subtyping Request Form
Blast 2.0 Server

National Centers for Disease Control
Biotechnology Core Facility Computing Laboratory


Procedure:

  1. To assign a type and subtype you should query the type specific database (default) using the form below with at least the first 240 bases obtained with primers emmseq2 or primer 1.
  2. Upon obtaining a perfect match (180/180) to an entry in the type-specific database, or identity to bases 31-180 combined with 3 or fewer mismatches to bases 1-30, you have identified the emm type and subtype of your strain.

If you encounter any new types or subtypes, please submit your unedited sequence traces along with your name/institution, and all information that you can provide concerning the isolate to bbeall@cdc.gov so that we can include your sequence and information in the CDC database and web site.

Information including any of the following (but not limited to it) is also greatly appreciated if you care to share it:

  • Your name and institution.
  • Isolate designation.
  • Country where isolated.
  • Year isolated.
  • Group carbohydrate (A ,C,G, etc).
  • Specimen (skin lesion, blood, throat, etc.).
  • Clinical manifestation (if any).
  • Multilocus sequence type
  • sof positive or negative.
  • opacity factor positive or negative.
  • bacitracin sensitivity
  • T antigen type.
  • spe gene profile.
  • other virulence determinants.
  • antibiotic resistance phenotypes/genotypes
  • GenBank designation (if you have it)

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

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

If you have questions please contact Bernard Beall at 404-639-1237 or bbeall@cdc.gov .

If you wish to enter 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 '.


Requestor:  
Phone: 
Email:
Sample Identifier:
For each of these, click only ONE button
Analysis Type:
Blastn
Blastp
Blastx
Database:
Full Length    
Type Specific
Number of Matches and Alignments included in the output:
10
50
100

Sequence in plain text format (spaces, numbers, and line feeds  are OK). Note that to receive proper alignments, your email font should be Courier or Courier new.

If you are sure the information is complete and correct, click on the ' Submit form ' button. You may scroll the form to make changes or click on the ' Clear fields ' button to clear all fields or cancel your request

 

Page last modified: February 8, 2008
Content source: National Center for Immunization and Respiratory Diseases
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