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Downloading Alleles from PubMLST

The video walkthrough can be found at the bottom of the page.

1. Go to pubmlst.org                     

pubMLST homepage

 2. Select "ORGANISMS"

Screenshot of PubMLST homepage with red box around organisms

 3. Select the organism you are looking at. 

Gene Starts WithOrganism
ACIN....Acinetobacter baumannii
CAMP....Campylobacter jejuni/coli
NEIS....Neisseria spp.

In this example we are looking at gene NEIS0051 so we will select Neisseria spp. The process is the same regardless of the organism. 

Screenshot of Organisms home with red box around Neisseria spp.

 4. Then select the blue box "Typing"

Screenshot of Neisseria page with red box around typing

5. Select the + sign next to "DOWNLOADS" on the right - clicking "DOWNLOADS" itself won't work

Screenshot of Neisseria typing page, with red box around downloads plus button

6. Then select the upper option "Allele Sequences"

Screenshot of pubmlst typing page, with red box around allele sequence in downloads

7. Then select "Alphabetical list"

Screenshot of PubMLST download allele page with red box around alphabetical list

8.    Next we search for our gene.
Use the Find function of your browser (usually Ctrl + F in Windows / Command + F in Mac)
Search for your gene: NEIS0051 for this example.
Click the download button to the right of it. The download will end in ".fas". Don't worry about duplicate search results - they are the same gene but under a different name.

Screenshot of alleles with red box around download button

 

 Walkthrough: 

The video discusses downloading the alleles for CAMP0021, from Campylobacter jejuni/coli. The walkthrough above is for NEIS0051, from Neisseria ssp. The process is the same for both, just select a different organism etc. 

To play the video, you need to accept cookies for videos.

Simplified - 

  1. Go to pubmlst.org 
  2. Select "Organisms"
  3. Select the organism you are looking at
  4. Select the blue box "Typing"
  5. Select the + sign next to "DOWNLOADS" on the right - clicking "DOWNLOADS" won't work
  6. Then select the upper option "Allele Sequences"
  7. Then select "Alphabetical list"
  8. Use the Find function of your browser (usually Ctrl + F in Windows / Command + F in Mac) to search for the gene.
    Select the download button to the right of it.