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RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

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  • HenryN
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    Originally posted by wotan View Post
    What would that mean?
    If it had H274Y, it would be Tamiflu resistant (but it doesn't have H274Y so it is sensitive).

    Leave a comment:


  • wotan
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    Originally posted by AlaskaDenise View Post
    I believe I'm see a "Y" in the NA of GQ293078!

    Influenza A virus (A/Zhejiang/2/2009(H1N1))


    Would someone more knowledgeable please check my work?

    .
    What would that mean?

    Leave a comment:


  • Commonground
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    Originally posted by AlaskaDenise View Post
    Dr. Niman just explained that we need to see a YYY in the area, not a YHY.

    So our tami meds still work (for now).

    Pheeew.

    .
    Thank you very much Alaska Denise. I really do appreciate the analysis. I don't understand it, and I really like the "bottom line".

    Leave a comment:


  • gsgs
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    see also here:

    http://www.biohealthbase.org/GSearch...antiViralTable


    http://www.biohealthbase.org/GSearch...ainDetailTable

    Leave a comment:


  • AlaskaDenise
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    Originally posted by niman View Post
    All sequences at NBCI that can be viewed by the public, are public - no permission required.
    So why would a sequence segment in the Riken site not show up in a search through the front-door to the NCBI site?

    A few days ago, it seemed to be a timing issue, i.e., that Riken had a more current update.

    .

    Leave a comment:


  • HenryN
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    Originally posted by AlaskaDenise View Post
    I have problems on the main NCBI page also. It doesn't appear to know about the same data that the Riken database is clearly extracting from NCBI. I'm assuming they have different permissions.

    I haven't learned how to use the other databases yet, so can't answer your questions on that.

    .
    All sequences at NBCI that can be viewed by the public, are public - no permission required.

    Leave a comment:


  • AlaskaDenise
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    Dr. Niman just explained that we need to see a YYY in the area, not a YHY.

    So our tami meds still work (for now).

    Pheeew.

    .

    Leave a comment:


  • gsgs
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    it's 275, not 274.
    274 is counting by another system, presumably N2

    Leave a comment:


  • AlaskaDenise
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    Originally posted by gsgs View Post
    genbank has them on the swine-flu page,
    although some of the records don't load.

    It's not yet available at the search page.........
    I have problems on the main NCBI page also. It doesn't appear to know about the same data that the Riken database is clearly extracting from NCBI. I'm assuming they have different permissions.

    I haven't learned how to use the other databases yet, so can't answer your questions on that.

    .

    Leave a comment:


  • mixin
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    Thanks to both of you for examining the sequences and sharing with us what you found. The more eyes, the better.

    Leave a comment:


  • AlaskaDenise
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    I left out the position I was referencing (obviously), I meant 274.

    Their "[NA of A/Zhejiang/2/2009(H1N1) : GQ293078] Mutation information"
    scroll down window on the lower right clearly reads " 274Y".

    If the mutation line format is confusing, it helps to read the "help" link on the 1st page - upper right top line.

    I await Mamabird's reading.

    .

    Leave a comment:


  • gsgs
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    Originally posted by AlaskaDenise View Post
    I believe I'm see a "Y" in the NA of GQ293078!

    Influenza A virus (A/Zhejiang/2/2009(H1N1))


    Would someone more knowledgeable please check my work?

    .

    I see a H : ...APNYHY...
    position 275

    Leave a comment:


  • gsgs
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    genbank has them on the swine-flu page,
    although some of the records don't load.

    It's not yet available at the search page.


    Does riken allow to download them all into one file ?



    http://mammalia.gsc.riken.jp/swine_influenza/

    Leave a comment:


  • AlaskaDenise
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    I believe I'm see a "Y" in the NA of GQ293078!

    Influenza A virus (A/Zhejiang/2/2009(H1N1))


    Would someone more knowledgeable please check my work?

    .

    Leave a comment:


  • AlaskaDenise
    replied
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    only 3 PB2s are shown and they are all an "E".

    .

    Leave a comment:

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