Making your own Submission File for GenBank

 


ver. 2.001          D-I-Y Submission File Maker          ©2012 Ian Logan

First select today's date          

Enter your surname. This becomes the submission filename
E.g. Entering 'Logan' will finally create 'logan.sqn'.

Enter the 'ethnicity' as you want to see it.
If in doubt - leave it blank. E.g. 'English', 'Scottish', 'Jewish'.

Enter the 'location' as you want to see it.
This can be your place of birth, or that of your maternal line.
E.g. 'England: London', 'USA: OK'
Enter in the format: 'country', 'colon', 'space', 'a state or city'.

Enter the haplogroup as you want to see it. E.g. 'H13a1', 'W'


     Next paste your FASTA sequence into this box and press

This window shows your final submission file



Instructions - for users of Microsoft WINDOWS

 

If you want to submit your mtFullSequence to GenBank you can use this Javascript program to make your own submission file.

BUT NOTE: YOU MUST HAVE HAD THE 'mtFullSequence' TEST AND BE A CUSTOMER OF FTDNA. You cannot submit just HVR1 & HVR2 results.

And, using this program you can only make a submission for yourself.

(If you want to make a submission of the mtFullSequence results for another person - I suggest you email me and discuss how to proceed.)

 

A little computer skill is needed - but if you take it carefully and slowly the process of making a submission file is not difficult.

So to proceed ....

 

1. Preparing the FASTA file.

   a. On your mtDNA Results Page locate the FASTA file download button.

       Follow the path: mtDNA > Print Certificate /Report Data > FASTA file

   b. Click on the download button and SAVE your FASTA file on your computer,

       making sure you know in which directory you have saved the file.

   c. Using Windows Explorer display the directory and locate the xxx.FASTA file (where xxx is your kit number).

   d. And rename your xxx.FASTA file to xxx.TXT, by rightclicking on the filename and using RENAME.

       (To the question, Are you sure you want to change it? Answer YES)

   e. Now leftclick on the xxx.TXT filename and the file should open in NOTEPAD or WORDPAD.

   f. Minimise this NOTEPAD window as you will need it later.

 

2. Entering the 5 other inputs needed for the program.

   a. DATE: In the above form change the date to "today's date".

   b. FILENAME: In the next box enter your surname - whilst any name can be used, I do suggest that you use your surname.

       (Note: Your surname will NOT appear on the final GenBank page.)

   c. ETHNICITY: Enter your choice here. May I suggest this is kept simple AND do make sure of the spelling.

       Suitable examples could be: English/Scottish/Jewish/Askenazi Jew/Native American.

       European/American/African/Caucasian/Asiatic are not very helpful and often it is appropriate to leave this entry blank.

   d. LOCATION: Enter your choice here. Again, keep it simple AND take care with the spelling.

       Try to be helpful and use the format 'Country: City'. If in any doubt leave it blank.

   e. HAPLOGROUP: Enter the haplogroup here. Use the label given by FTDNA, or one from www.phylotree.org, if you prefer.

 

3. Transferring the FASTA file.

   a. Display your xxx.TXT file and leftclick in the window to show the cursor.

   b. Use CTRL-A to highlight the contents of the file, followed by CTRL-C to capture the contents.

   c. Again minimise the NOTEPAD window and display the entry form once again.

   d. Move the cursor to the FASTA file entry box and leftclick to enter the cursor and use CTRL-V to paste your FASTA file into the box.

       At this stage the FASTA file box should contain a copy of the FASTA file

       with the first line reading similar to '>A1234,HVR2,CR,HVR1' and the bottom lines ending with 'CATCACGATG'.

       DO TAKE CARE SO AS NOT TO CORRUPT THE CONTENTS OF THIS BOX !

 

4. Executing the Javascript program.

   a. It is now time to execute the program, so press SUBMIT.

       And ... the text of the submission file should appear in the lower box.

       By all means look at the submission file, and again DO TAKE CARE SO AS NOT TO CORRUPT THE CONTENTS OF THIS BOX !

       And if you have any concerns, press CLEAR BOXES and repeat the procedure.

 

5. Transferring the Submission file.

   a. Note the Submission file starts with    Seq-submit ::= {    and finishes with    'H } } } }

   b. Next move the cursor to the Submission file box and leftclick to enter the cursor.

   c. And, use CTRL-A, and CTRL-C to capture the all the text of the submission file

   d. Now open a new NOTEPAD window by using START, ALL PROGRAMS, ACCESSORIES, NOTEPAD

   e. Move the cursor to the new NOTEPAD window, leftclick to enter the cursor and use CTRL-V to paste your submission file into the box.

   f. Check once more that the Submission file starts with    Seq-submit ::= {    and finishes with    'H } } } }

   g. Now use FILE and SAVE AS ... to save the submission file using the same filename you used at 2b, BUT MOST IMPORTANTLY use the filetype .sqn

      For example: If the filename was

      logan

      save the file ALL IN LOWER CASE characters as

      logan.sqn

      Again make sure of which directory you are using.

   h. Now open the directory and check you can find the file.

      And, if the filename appears as   xxx.sqn.txt   use RENAME to change it to   xxx.sqn

 

6. Emailing GenBank.

   a. Create a new email to: gb-sub@ncbi.nlm.nih.gov

   b. Enter a subject, such as 'GenBank Submission - xxx.sqn'

   c. And at this stage attach your    xxx.sqn    file by using 'Insert' and 'File as attachment...' (or whatever is appropriate on you email program).

   d. In the body of the email write something like:

      Susan Schafer

      I attach my submission file for GenBank, named 'xxx.sqn'.

      It is for my mitochondrial DNA sequence and the sequence has not been published in any other database.

      My FTDNA Kit number is 'xxxxx', and I accept it will appear on my GenBank page.

      Thank you

      (and your full name)

   e. Please note that normally your surname will not appear on the final GenBank page.

   f. Finally: when you are totally happy, send the email.

 

7. The process afterwards.

   a. After submitting your email you will get several emails from GenBank.

   b. A receipt will be sent almost immediately.

   c. Followed a couple of days later by an email asking you to re-confirm the sequence is yours.

      Reply to this email to say you are happy to proceed.

   d. An email giving your Accession number.

   e. Finally some days later, an email containing a 'flat file' - which is a 'proof' copy of your page - and your publication data.

      Make a final check of the 'flat file' to see it contains the correct information.

 

8. Publication.

   a. On publication date your sequence should be viewable on GenBank, by entering your Accession number.

   b. However, it will be 2-4 days before the sequence is indexed and can be found

      by using a search string, such as:    "Homo sapiens" [ORGANISM] "complete genome" mitochondrion

 

9. Revising a GenBank page

      It is to be hoped that a GenBank page never needs revision, but there are several reasons why it might.

      However, revision should NOT be undertaken just to change the haplogrouping as new subgroups are defined.

      But if there is an overt error on the GenBank page, or FTDNA amends the results, then revision will be appropriate.

 

   So if revision is necessary the required steps will be:-

   a. Follow the steps above, correcting the error, and make a fresh submission file, with the filename, for example:

      logan2

   b. Create a new email to: gb-admin@ncbi.nlm.nih.gov

   b. Enter a subject, such as 'Revision of my GenBank Submission - Accession Number XXnnnnnn'

   c. And at this stage attach your    xxx2.sqn    file by using 'Insert' and 'File as attachment...' (or whatever is appropriate on you email program).

   d. In the body of the email write something like:

      Susan Schafer

      I am sorry for the inconvenience but my earlier submission for my GenBank entry with Accession Number XXnnnnnn needs to be revised.

      I attach a corrected submission file, named 'xxx2.sqn'.

      This is required as the earlier submission had an error (specify, eg. FTDNA has amended the sequencing).

      The submission file is for my mitochondrial DNA sequence and the sequence has not been published in any other database.

      Thank you

      (and your full name)

   e. And send the email.

 

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Revision history for this program

11 Apr 2010   Version 1.001 - 1.003   Launch & some initial bugs exposed.

11 Apr 2010   Version 1.004   Working program.

11 Apr 2010   Version 1.005   Warning messages removed.

12 Apr 2010   Version 1.006   More instructions and the uncommon heteroplasmy codes added.

12 Apr 2010   Version 1.007   Instructions about revising a GenBank page added.

15 Apr 2010   Version 1.008   Improved handling of ethnicity and location data.

24 Apr 2010   Version 1.009   Check added for presence of 'HVR2,CR,HVR1' in FASTA file.

16 Jun 2010   Version 1.010   Date changed.

19 Jun 2010   Version 1.011   Instruction to include Kit Number added.

1 Jul 2010   Version 1.012   Error in handling heteroplasmy corrected.

13 Jul 2010   Version 1.013   Fresh instructions for finding FASTA file.

3 Nov 2010   Version 1.014   New instruction concerning kit numbers.

16 Apr 2011   Version 1.015   Change of date and version number.

9 Jun 2011   Version 1.016   Additional instructions.

3 Jun 2011   Version 2.001   Various changes.

4 Jun 2013   Version 2.001   Notifying FTDNA dropped.

 

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IF YOU HAVE ANY QUESTIONS   -   CONTACT ME ON:   ianlogan22@btinternet.com