Announcement

Collapse
No announcement yet.

Have you submitted your MtFullSequences to Genbank?

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #31
    Originally posted by GayeSherman View Post
    My problem is I don't remember if I submitted anything to GenBank and I wouldn't remember my accession number if I did.
    Do I recall correctly that you have quite a number of FMS matches? If so, it probably doesn't matter too much whether you're in GenBank or not. The number of identical sequences can help date the origin of the subclade, but your contribution wouldn't affect the calculations too much either way.

    Comment


    • #32
      Please Submit Your Full Genome Sequence to GenBank,National Center for Biotechnology

      I want to ask you to submit your Full Genome Sequence as I did:

      Homo sapiens haplogroup H3 mitochondrion, complete genome
      http://www.ncbi.nlm.nih.gov/nuccore/JN020360

      FOR FAMILY TREE DNA USERS
      A common file format used for the storage and transfer of DNA sequences are FASTA files. Your FASTA file contains your raw mtDNA sequence.
      On Family Tree DNA under "mtDNA" is the option:
      "Print Certificate/Report/Data."

      This page contains links to download your various result files and certificates. The link with the file for your data is labeled "FASTA File - FASTA" If you click on the highlighted "FAST File," you should get a request to download the file. Remember which file directory you save it in.

      This FASTA file is not in the format used by GenBank. It must be transferred into a .sgn file.
      You can send your .FASTA file to Ian Logan, mtDNA [email protected] .
      http://www.ianlogan.co.uk/checker/genbank.htm

      You can either use my directions here or follow his there.
      FOR DETAILS ON SUBMITTING YOUR OWN SEQUENCE TO GENBANK - Click here
      http://www.ianlogan.co.uk/Submission.htm

      They are very detailed and not intended for those with access to their own files. I have included my FASTA file to illustrate an example of the file you are looking for.

      Ian Logan has a quick turnaround, so you should receive your file back in about 72 hours. When you get it back, it will look like my scharf.sqn file.
      At that point, you send it to:
      Susan Schafer PhD GenBank Direct Submission Staff
      [email protected]

      GenBank will give out an Accession number, and you can expect
      publication in about 14-21 days.

      In my case, I submitted my FASTA file to Ian Logan on May 18th. He sent me the .sqn file on May 20th, which I sent to Doctor Susan Shaffer immediately. She sent me a couple of emails and it was published on June 6th. My results may not be typical.

      Comment


      • #33
        Hello all,

        For those of you that have submitted your Full Sequence mtDNA survey agreeing to let Family Tree DNA use your results in research, we will upload the results to GenBank IF your results are used for and published in the research (anonymously as supporting data). Otherwise Family Tree DNA will not upload your results to Gen Bank, but you are welcome to do this on your own at any time.

        If you choose to upload your results to Gen Bank on your own or through another researcher such as Ian Logan, please email [email protected] with your Gen Bank ID number, so we can try to avoid any potential for duplicate entries in the database, (please also include your kit number in this email).

        -Darren Marin
        Family Tree DNA

        Comment


        • #34
          If upload your results to Gen Bank on your own or another researcher.

          I notified Bennett Greenspan about it previously. I have notified the Help Desk and Ian Logan now as well. Perhaps he can catch the others up on that issue of notifying you.

          Originally posted by Darren View Post
          Hello all,

          For those of you that have submitted your Full Sequence mtDNA survey agreeing to let Family Tree DNA use your results in research, we will upload the results to GenBank IF your results are used for and published in the research (anonymously as supporting data). Otherwise Family Tree DNA will not upload your results to Gen Bank, but you are welcome to do this on your own at any time.

          If you choose to upload your results to Gen Bank on your own or through another researcher such as Ian Logan, please email [email protected] with your Gen Bank ID number, so we can try to avoid any potential for duplicate entries in the database, (please also include your kit number in this email).

          -Darren Marin
          Family Tree DNA

          Comment


          • #35
            How do I post DNA results for comparison?

            I had my 92yr old dads DNA tested by ancestry.com, but unfortunately there hasn't been any Russells to show a match. I was told to transfer his test results to this site because there was a Russell DNA forum here so I'm trying to find out how to do this. The documentation I have shows I'm from the bloodline of Bryce Russell married to Jane Thompson so I'm hoping someone can HELP ME. I will appreciate any input since I'm completely new to the DNA comparison side of ancestry.

            Comment


            • #36
              Originally posted by russe386 View Post
              I had my 92yr old dads DNA tested by ancestry.com, but unfortunately there hasn't been any Russells to show a match. I was told to transfer his test results to this site because there was a Russell DNA forum here so I'm trying to find out how to do this. The documentation I have shows I'm from the bloodline of Bryce Russell married to Jane Thompson so I'm hoping someone can HELP ME. I will appreciate any input since I'm completely new to the DNA comparison side of ancestry.
              Hi. Here's the Russell project

              http://www.worldfamilies.net/surnames/russell/

              I'd try contacting the project admistrator. I'm sure they can probably help you.

              Another thing you might try is entering your father's results into ysearch.org.

              Comment


              • #37
                U5b2b* submitted to GenBank

                Kit#188035
                Well it's been a year Sep 2010 since I took my mtDNA full sequence and still no matches all across the board I don't know whether to be confused or disappointed.

                Rec'd my 1st email Aug 11, 2011 from FTDNA suggesting that I submit to GenBank:
                "FTDNA placed you in group U5b2b*. You have all of the mutations that
                define U5b2b, and the "star" indicates that you are not part of any of
                the currently named daughter groups of U5b2b. But you do have 7
                additional, unique mutations for U5b2b that will define a new daughter
                group of U5b2b".

                HVR1: 16261T; 16270T; 16320T
                HVR1: 73G; 150T; 189G; 263G; 315.1C
                CR differences from CRS: 750G; 1438G; 1721T; 2626C; 2706G; 3197C; 4659A; 4769G; 7028T; 7768G; 8860G; 9477A; 11467G; 11653G; 11719A; 12308G; 12372A; 12634G; 13617C; 13630G; 13637G; 13759A; 14182C; 14766T; 15299C; 15326G.

                My yDNA is: R1b1b2a1b5 type III.

                My mtDNA U5b2b* is now posted on GenBank so I suppose it now a waiting period to see if there will be any matches to comes.

                I only know my genealogical heritage based on documented research. My mother's HUNT paternal lineage are connected to the Melungeon and Lumbee clans of NC. Her maternal lineage ROGERS, KOON/KUHN, and FROST I've document as for back of 1810 Richland Co., SC. Her earliest female Mary Ann UNKN, m/t Daniel Henry FROST b. abt 1808 SC are noted on the Freedmon Rolls associated with mixed raced persons of color owning land during that time period. The 1850 up to the 1880 records indicate my FROST family are indicated as mulatto. Their daughter my great grandmother Mary Ann FROST "mulatto" married Osborne Edward KOON "white" so therefore on the 1900 and forward they are indicated as white. Osborne Edward KOON is a direct descendant of Han Casper KUHN of Switzerland.

                Hopefully someone will read this and will have a connection to me
                Thank you

                Comment


                • #38
                  About Genbank

                  Hello!

                  Does anybody help me to submit my result of mtDNA FGS to Genbank?

                  FGSV.

                  Comment


                  • #39
                    Originally posted by FGSV View Post
                    Hello!

                    Does anybody help me to submit my result of mtDNA FGS to Genbank?

                    FGSV.
                    Hi FGSV and all,

                    Most use Ian Logan's do-it-yourself method: http://www.ianlogan.co.uk/checker/submission_maker.htm

                    Or if you need assistance: http://www.ianlogan.co.uk/Submission.htm

                    Please let FTDNA and your mtDNA haplogroup project administrator your GenBank accession number when you get it.

                    Bill Hurst

                    Comment


                    • #40
                      feautre annotation?

                      Would anyone by chance know how to create a Feature Annotation to a sequence? that's the part in the Genbank record right before the actual sequence. The feature annotation looks like this:

                      D-loop complement(join(16029..16570,1..579))

                      tRNA 579..649
                      /product="tRNA-Phe"
                      rRNA 650..1603
                      /product="12S ribosomal RNA"
                      tRNA 1604..1672
                      /product="tRNA-Val"
                      rRNA 1673..3230
                      /product="16S ribosomal RNA"
                      tRNA 3231..3305
                      /product="tRNA-Leu"
                      /note="codons recognized: UUR"
                      gene 3308..4263
                      /gene="ND1"
                      CDS 3308..4263

                      etc.

                      Is there some (preferably free...) software where I can enter my sequence and then have the annotation come up? Either in this format, or even better, 5 column tab delimited format...Or any format.
                      (This is the part that annotates where to find the different genes etc in the sequence).

                      thanks everyone. I think i better post this in its own message, too, so that it doesn't get lost.

                      Sammi

                      Comment


                      • #41
                        Just submitted yesterday to gen bank.

                        Pamela

                        Comment


                        • #42
                          Submitted mine through Ian Logan a few years back. Never got an email from FTDNA, never got the survey.

                          Having read this thread, I am still not clear about FTDNA's purposes or procedures for submission of customer FGS to GenBank.

                          I think submission of FGS to GenBank is important and urge any others considering it to take the Ian Logan route as the more reliable means.

                          Comment


                          • #43
                            Originally posted by tomcat View Post
                            Submitted mine through Ian Logan a few years back. Never got an email from FTDNA, never got the survey.

                            Having read this thread, I am still not clear about FTDNA's purposes or procedures for submission of customer FGS to GenBank.

                            I think submission of FGS to GenBank is important and urge any others considering it to take the Ian Logan route as the more reliable means.
                            Agreed. Important to do this.

                            My 2 cents about "never got email" etc. I followed the route via Ian Logan a few months back, and heard nothing. A couple of weeks ago, I asked Ian if he had a record of it. He did not. So I went through the procedure, via Ian again, and this time I got several follow-up emails and an accession number, and a date of publication etc etc. Somewhere along the line in my first submission, it ran off the rails and none of us were any the wiser. Lesson: If you don't end up with an Accession number, and a publication date (after a couple of weeks maybe), your submission is 'lost in space'.

                            I also noted that FTDNA had been notified by Genbank. As a matter of course, I had also advised FTDNA (as suggested by Ian.)

                            BTW, Ian is friendly, helpful and efficient !
                            .

                            Comment


                            • #44
                              Haplogroup H > H31

                              I had long been uninspired and a bit overwhelmed by the designation of "H" as a haplogroup. It seemed unbelievable that I could be in the "most common" European group, matching people in all of Europe, and many continents the Europeans populated, yet have only 12 FGS matches. The numbers just didn't add up.

                              In using tools discovered on these forums, I find that my sequence is actually in haplogroup H31 and not so "common" after all. According to Ian Logan, there are only 5 (!!) published sequences in H31.

                              The moral of the story is that the FTDNA (and 23andMe) designation may not be the most complete or current information available.

                              Those who are curious should pursue more information, not be afraid to ask questions, and continue seeking.

                              So, even though the mtdna testing I have done has not proven to be useful to my personal genealogy as I had originally hoped, and has shed very little light on my deeper ancestral roots or ethnicity, it could still contribute to the public knowledge base.

                              I also sent my 12 FGS matches a note advising them of this "discovery" and inviting them to consider submitting to genbank as well. My own submission is still in process, but has been received.

                              Back to "wait and see" and seek when I can.

                              Comment


                              • #45
                                Originally posted by AngeliaR View Post
                                The moral of the story is that the FTDNA (and 23andMe) designation may not be the most complete or current information available.

                                Those who are curious should pursue more information, not be afraid to ask questions, and continue seeking.

                                So, even though the mtdna testing I have done has not proven to be useful to my personal genealogy as I had originally hoped, and has shed very little light on my deeper ancestral roots or ethnicity, it could still contribute to the public knowledge base.
                                Well put, AngeliaR.

                                The public knowledge base is very important, and even if it does not help us as individuals when we contribute, those following will have a better time of it.

                                Not that FTDNA needs defending - but I think the (conservative?) designations may also be guided by 'firm', as opposed to 'draft', phylotrees. I have seen several variations of my U3b HG proposed, depending on what I read, from whom, and how the FGS is read. U3b is a small group anyway, but I feel my results will be further refined after the next 'official' update.

                                Comment

                                Working...
                                X