Step 1: Open your FASTA file. For Family Tree DNA customers, visit your "MyFTDNA" page - click on the "mtDNA Results" tab and then the blue "FASTA" file link at the top of the page just below the title tab. This will generate a results page in raw sequence format. Save the file to a folder on your computer. You may also choose to open and save the file in a text editor like notepad for Windows or TextEdit for Mac.

Fig 1:

Step 2: Open Genbank

Step 3: Either click "Upload File" or copy and paste² your FASTA code into the box "Enter accession number, gi, or FASTA sequence" then click on "Nucleotide collection" in the drop down menu and leave the radio button checked on "Highly similar sequences (megablast)" then click the "BLAST" button. (Fig 2)

Fig 2:

Step 4: When the page loads, scroll down and view the list "Sequences producing significant alignments" which should list mtDNA haplotypes that have been uploaded which match, or are a close match to yours.³ Click the "Accession" number and it will give you the study in which that haplotype was published.

BLASTING FGS with the Greasemonkey Tool (Firefox browser only)

Step 1: Confirm that the Firefox browser is loaded on your computer. If not, download here.

Step 2: Visit Ian Logan's site and download Greasemonkey.  When Greasemonkey is installed, you will see a small monkey face in the lower right corner of your Firefox browser.

Step 3: Paste the following user script into the browser:
www.ianlogan.co.uk/scripts/analyser.user.js
(NOTE:  If you have downloaded Ian's script on a previous occasion, you may need to do so again for current updates.)

and hit the install key on the box that pops up. (Fig 3)

Fig 3:

Step 4: Open Genbank in Firefox.  Highlight, copy and paste² your FASTA code into the box titled "Enter accession number, gi, or FASTA sequence" then click on "Nucleotide collection" in the drop down menu under "CHOOSE SEARCH SET" and leave the radio button checked on "Highly similar sequences (megablast)" then click the "BLAST" button.

Step 5: Wait while the database is searching.  When the pages appears, scroll down past the "Color Key for alignment scores" table, and click an accession number hyperlink in the next table.

Step 6: Under the "Display" drop down menu, click on "FASTA".  The raw sequence will appear, but to the right, a Greasemonkey box will also appear that converts the FASTA to a mitochondrial haplotype that lists the differences from the CRS. (Fig 4) These differences are the ones uploaded from the paper that you clicked the accession number for, and is useful for comparing to your own FGS results. 

Fig 4:

¹Participants in scientific studies are anonymous.

²To copy and paste, highlight just the FASTA results by holding down your left mouse button and running it across the text and then click on "Edit" in the top of your browser window, then click "Copy".

³Tip: Clicking the link above the "Accession" table (below the "Color key for alignment scores" table) labeled "Distance tree of results" will produce a phylogenetic tree comparing your results to those in Genbank.

Sources:
'Greasemonkey' and a new mtDNA 'ONLINE ANALYSER'

With deep appreciation to Ian Logan!
Contribution credits: 
K. Borges, R. Canada, P. Malysz, C. Vass, D. Miller
Copyright © 2006-2008
isogg.org
All Rights Reserved
Compiled: 11/01/07
Page last updated: 02/21/2008
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