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diversity in avian influenza in the 8 segments

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  • diversity in avian influenza in the 8 segments

    considering each segment separately
    ignoring reassortment
    ~1000 random viruses from each segment

    1 virus-segment per line
    one position per row
    black-pixel=difference from the average = consensus

    virus-segments and positions are sorted, so that the pixels cluster best

    (I may add some characterization later ....
    big black area is usually H5N1, ~60% American, ~40%Eurasian
    without big black areas = early viruses,

    Brevig 1918 should later be marked in each segment

    -------------------------------

    you can spot the 16 HA types in segment 4
    the 9 NA-types in segment 6
    the 2 NS-types in segment 8

    and the North-American, Eurasian separation in each segment

    America has more mallard samples, Asia more poultry samples

    (sequences from genbank, aligned with mafft)
    Attached Files
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

  • #2
    Re: diversity in avian influenza in the 8 segments

    paper about NA stalk deletions:

    http://www.plosone.org/article/info%...l.pone.0014722

    pdf: http://www.plosone.org/article/fetch...esentation=PDF

    9 pages, 70 references , Feb.2011



    NA aa 30-90 deletion patterns for 9087 full avian NAs at genbank :
    (when alignerd with mafft)

    count,pattern,NA-type
    Code:
       2008,OOOOOOOOOOOOOOOOOOO--------------------OOOOOOOOOOOOOOOOOOOOOO---1
       1893,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---2
       1369,OOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---6
       1353,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---8
       1047,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---1
        698,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---3
        508,OOOOOOOOOOO--OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---7
        401,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---9
        293,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO----OOOOOOOOOOOOOOOOOOOOOOOOO---2
        269,OOOOOOOOOOOOOOOOOOOOOOOOOOO----------------OOOOOOOOOOOOOOOOOO---2
        218,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---4
        183,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---5
         91,OOOOOOOOOOOOOOOOOOOOOO-------------------OOOOOOOOOOOOOOOOOOOO---1
         88,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---7
         69,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---------------------OOOOOOOO---2
         58,OOOOOOOOOOOOOOOOOOOOOOO-----------------------OOOOOOOOOOOOOOO---1
         52,OOOOOOOOO--OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---5
         30,OOOOOOOOOOOOOOOOOOOOOOOOO------------------------OOOOOOOOOOOO---3
         27,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO--------------------OOOOOOOO---2
         26,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO----------OOOOOOOOOOOO---2
         25,OOOOOOOOOO-------------OOOOOOOOOOOOOO---OOOOOOOOOOOOOOOOOOOOO---1
         18,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---------------------OOOOOOO---2
         18,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO------------------OOOOOOOOOOOO---2
         16,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO-----------OOOOOOOOOOOOOOO---2
         14,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOOO---9
         12,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO--OOOOOOOOOOOO---3
         12,OOOOOOOO--OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---2
          9,OOOOOOOOOOOOOOOOOOO-------OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---2
          9,OOOOOOOOOO-------------OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---1
          7,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---6
          7,OOOOOOOOOOOOOOOOOOOOOOOOOOOO-------------------------OOOOOOOO---2
          7,OOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOOO-OOOOOOOOOOOOOOOOOOOOOOOO---6
          6,OOOOOOOOOOOOOOOOOO-----------------------OOOOOOOOOOOOOOOOOOOO---2
          6,OOOOOOOOOOOO--------------------------OOOOOOOOOOOOOOOOOOOOOOO---6
          6,OOOOOOOOO--OOOOOOOOOOOOOOOOOOOOOOOOOOOOOO----OOOOOOOOOOOOOOOO---5
          3,OOOOOOOOOOOOOOOOOOOOOOOOOOOO----------------------OOOOOOOOOOO---2
          3,OOOOOOOOOOOOOOOOOOOOOOO----------------------OOOOOOOOOOOOOOOO---1
          3,OOOOOOOOO-OOOOOOOOO--------------------OOOOOOOOOOOOOOOOOOOOOO---1
    
          2,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO------OOOOOOOOOOOOOOOOOO---9
          2,OOOOOOOOOOOOOOOOOOOOOOOOOOO--------------OOOOOOOOOOOOOOOOOOOO---2
          2,OOOOOOOOOOOOOOOOOOOOOOOO---------------------OOOOOOOOOOOOOOOO---1
          2,OOOOOOOOOOOOOOOOOOOOOOO-------------------------OOOOOOOOOOOOO---2
          2,OOOOOOOOOOOOOOOOOOOOO-------------OOOOOOOOOOOOOOOOOOOOOOOOOOO---2
          2,OOOOOOOOOOOOOOOOOOOO----------------------------OOOOOOOOOOOOO---3
          2,OOOOOOOOOOOOOOOOOOO--------------------OOOOO-OOOOOOOOOOOOOOOO---1
          2,OOOOOOOOOOOOOOOO-----OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---2
          2,OOOOOOOOOOO--OOOOOOOOOOO-----------------------OOOOOOOOOOOOOO---7
          2,OOOOOOOOOOO-------------------------OOOOOOOOOOOOOOOOOOOOOOOOO---3
          2,OOOOO-OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---8
    
          1,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOO---5
          1,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOOOO---9
          1,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOOOOO---2
          1,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOOOOOO---8
          1,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOOOOOOO---8
          1,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOOOOOOO---3
          1,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO-----OOOOOOOOOOOOOOOOO---9
          1,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---------OOOOOOOOOOOOOOO---2
          1,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOOOOOOOOOOO-OOOOOOO---2
          1,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO----------------OOOOOOOOOOO---2
          1,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO--OOOOOOOOOOOOOOOOOOOOOOOOOO---2
          1,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOOOOOOOOOOOOOOOOOOOOO---3
          1,OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO--------------------OOOOOOOOO---2
          1,OOOOOOOOOOOOOOOOOOOOOOOOOO--------------------------OOOOOOOOO---2
          1,OOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---4
          1,OOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---3
          1,OOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOOOOOOO---------------OOOOOO---6
          1,OOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOO-----------------------OOOOOO---6
          1,OOOOOOOOOOOOOOOOOOOOOOOOO-OOOOO---------OOOOOOOOOOOOOOOOOOOOO---6
          1,OOOOOOOOOOOOOOOOOOOOOOOOO-OOOO------------OOOOOOOOOOOOOOOOOOO---6
          1,OOOOOOOOOOOOOOOOOOOOOOOOO-OOO-OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---2
          1,OOOOOOOOOOOOOOOOOOOOOOOOO-OOO------------OOOOOOOOOOOOOOOOOOOO---6
          1,OOOOOOOOOOOOOOOOOOOOOOOOO-OO-OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---6
          1,OOOOOOOOOOOOOOOOOOOOOOOO------------------OOOOOOOOOOOOOOOOOOO---1
          1,OOOOOOOOOOOOOOOOOOOOOOOO-------------------OOOOOOOOOOOOOOOOOO---2
          1,OOOOOOOOOOOOOOOOOOOOOOO------------OOOOOOOOOOOOOOOOOOOOOOOOOO---6
          1,OOOOOOOOOOOOOOOOOOOOOOO-------------OOOOOOOOOOOOOOOOOOOOOOOOO---6
          1,OOOOOOOOOOOOOOOOOOOOOOO-------------------------OOOOOOOOOOOOO---3
          1,OOOOOOOOOOOOOOOOOOOOOO----------------OOOOOOOOOOOOOOOOOOOOOOO---3
          1,OOOOOOOOOOOOOOOOOOOO-OOOOOO----------------OOOOOOOOOOOOOOOOOO---2
          1,OOOOOOOOOOOOOOOOOOOO------------------------OOOOOOOOOOOOOOOOO---2
          1,OOOOOOOOOOOOOOOOOOO--------------------OOOOOOOOOOOOOOOOOO-OOO---1
          1,OOOOOOOOOOOOOOOOOOO--------------------OOOOOOOO--OOOOOOOOOOOO---1
          1,OOOOOOOOOOOOOOOOOOO--------------------OOO----OOOOOOOOOOOOOOO---1
          1,OOOOOOOOOOOOOOOOOOO--------------------OO--OOOOOOOOOOOOOOOOOO---1
          1,OOOOOOOOOOOOOOOOOOO--------------------O-OOOOOOOOOOOOOOOOOOOO---1
          1,OOOOOOOOOOOOOOOOOO-----------------------OOOOOOOOOOOOOOOOOOOO---8
          1,OOOOOOOOOOOOOOOOOO-------------------------OOOOOOOOOOOOOOOOOO---1
          1,OOOOOOOOOOOOOOOOO-OOOOOOOOO----------------OOOOOOOOOOOOOOOOOO---2
          1,OOOOOOOOOOOOOOOO-OOOOOOOOOO----------------OOOOOOOOOOOOOOOOOO---2
          1,OOOOOOOOOOOOOO------OOO--------------------OOOOOOOOOOOOOOOOOO---2
          1,OOOOOOOOOOOOOO------------------OOOOOOOOOOOOOOOOOOOOOOOOOOOOO---2
          1,OOOOOOOOOOOOOO------------------------OOOOOOOOOOOOOOOOOOOOOOO---1
          1,OOOOOOOOOOOOOO--------------------------OOOOOOOOOOOOOOOOOOOOO---6
          1,OOOOOOOOOOOOOO---------------------------OOOOOOOOOOOOOOOOOOOO---2
          1,OOOOOOOOOOOOOO-----------------------------OOOOOOOOOOOOOOOOOO---2
          1,OOOOOOOOOOOOO------------------------OOOOOOOOOOOOOOOOOOOOOOOO---1
          1,OOOOOOOOOOOO-OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---2
          1,OOOOOOOOOOOO-OOOOOOOOOO-----------------------OOOOOOOOOOOOOOO---1
          1,OOOOOOOOOOOO-OOOOOO--------------------OOOOOOOOOOOOOO-OOOOOOO---1
          1,OOOOOOOOOOO--OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO-OOOOOOOOOOOOO---7
          1,OOOOOOOOOOO--OOOOOOOOOO-------------------OOOOOOOOOOOOOOOOOOO---7
          1,OOOOOOOOOO-------OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---2
          1,OOOOOOOO-OOOOOOOOOOOOOOOOOO----------------OOOOOOOOOOOOOOOOOO---2
          1,OOOOOOOO-OOOOOOOOOO--------------------OOOOOOOOOOOOOOOOOOOOOO---1
          1,OOOOOOO-OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---3
          1,OOOOOOO-OOOOOOOOOOOOOOOOOOO----------------OOOOOOOOOOOOOOOOOO---2
          1,OOOOOO----------------------------OOOOOOOOOOOOOOOOOOOOOOOOOOO---3
          1,OOOOO-OOOOOO-------------------OOOOO-OOOOOOOOOOOOOOOOOOO-OO-O---6
          1,OOOO-OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---2
          1,OOO-OOOOOOOOOOOOOO-OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---7
          1,O-OOOO-OOOOOOOOOOOOOOOOOOOO-OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO---8
          1,-------OOOOOOOOOOOOOOOOOOOOOOOOO----OOOOOOOOOOOOOOOOOOOOOOOOO---2
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

    Comment


    • #3
      Re: diversity in avian influenza in the 8 segments

      I built 32=1+1+1+16+1+9+1+2 aligned flu-files bitsc* , sorted by date,
      with a total of 116229 avian influenza viruses from genbank 2014/12/09.
      I can upload or send, if there is interest

      196MB uncompressed, 4.3MB when compressed with 7zip

      xx sequences were sorted out as "bad" , distant from other sequences
      in that file, probably incorrectly declared=assigned to the files.
      Others were corrected, main problem : insertion or deletion of
      one nucleotide


      13412+13357+13371+19559+13022+15700+14157+13665 , genbank
      13412+13361+13372+19551+13021+15690+14142+13680 , aligned

      some few sequences may appear twice in the aligned files




      m=116243 n=:1640


      1,m=13412 n=:2282
      2,m=13361 n=:2276
      3,m=13372 n=:2153
      4,m=19559 n=:1640
      5,m=13021 n=:1499
      6,m=15700 n=:99
      7,m=14142 n=:984
      8,m=13680 n=:840
      ---------
      116247


      4,m=19559 n=:1640
      41,m= 708 n=:1703
      42,m= 500 n=:1691
      43,m=2012 n=:1703
      44,m=1763 n=:1700
      45,m=5787 n=:1718
      46,m=1777 n=:1706
      47,m=1706 n=:1718
      48,m= 177 n=:1703
      49,m=3310 n=:1685
      4a,m= 777 n=:1688
      4b,m= 606 n=:1700
      4c,m= 202 n=:1697
      4d,m= 137 n=:1703
      4e,m= 20 n=:1709
      4f,m= 15 n=:1715
      4g,m= 54 n=:1700
      -----------
      19551

      6,m=15700 n=:99
      61,m=4646 n=:1412
      62,m=3979 n=:1412
      63,m=1000 n=:1412
      64,m= 292 n=:1415
      65,m= 388 n=:1424
      66,m=2018 n=:1418
      67,m= 883 n=:1418
      68,m=1731 n=:1415
      69,m= 753 n=:1415
      ---------
      15690

      8,m=13680 n=:840
      81,m=10609 n=:840
      82,m=3071 n=:840
      ---------
      13680


      [m=number of sequences, including partials, coding region
      n-2= nucleotides-length in that alignment]



      to be added : average and maximal #nucleotide differences in each
      of the 32 files from the index = average nucleotide at each position
      [done]

      mutation-pictures of 1000 randomly selected full sequences from
      each of the 32 files
      splitting of the files into American and Eurasian

      average and minimal distance(year) of the American and Eurasian parts

      amino-acid files
      updated cloud pictures (dSyn. vs. dNonsyn. in 2d)

      Code:
      filename
      average distance from the index(average) of that file in 1/100 percent
      number of sequences (including partials)
      maximum distance from the index of that file in 1/100 percent
      
      bitsc1, 933 , 13412 , 1906 
      bitsc2, 681 , 13361 , 2265     13360,1785    NZ
      bitsc3, 684 , 13372 , 1761 
      bitsc5, 679 , 13021 , 1740 
      bitsc7, 476 , 14142 , 1310 
      bitsc41, 638 , 708 , 3003        686,1575   swine H1N1-->turkey
      bitsc42, 834 , 500 , 1612 
      bitsc43, 865 , 2012 , 2238       1991,1666   swine H3N2 --> turkey
      bitsc44, 811 , 1763 , 1965 
      bitsc45, 577 , 5787 , 2733      5692,2170   partials Mex.H5N2
      bitsc46, 923 , 1777 , 2511 
      bitsc47, 1299 , 1706 , 2394 
      bitsc48, 605 , 177 , 1499 
      bitsc49, 743 , 3310 , 1902 
      bitsc4a, 665 , 777 , 2139 
      bitsc4b, 835 , 606 , 2248 
      bitsc4c, 662 , 202 , 1893 
      bitsc4d, 1220 , 137 , 1804 
      bitsc4e, 472 , 20 , 986 
      bitsc4f, 137 , 15 , 1062 
      bitsc4g, 881 , 54 , 1584 
      bitsc61, 586 , 4646 , 2277 
      bitsc62, 802 , 3979 , 1707 
      bitsc63, 797 , 1000 , 2840          956,1604  (H16N3 gulls)
      bitsc64, 756 , 292 , 1748 
      bitsc65, 784 , 388 , 2959           386,2138
      bitsc66, 1043 , 2018 , 2547    1975,2147
      bitsc67, 902 , 883 , 2877 
      bitsc68, 636 , 1731 , 2677       1729,2439
      bitsc69, 590 , 753 , 2127 
      bitsc81, 506 , 10609 , 1634 
      bitsc82, 402 , 3071 , 1539
      Attached Files
      I'm interested in expert panflu damage estimates
      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

      Comment


      • #4
        updates including the new H7Nx files from 2015/03/13 is available
        14560+14596+14609+21221+14256+17097+15370+14935=12 6644 avian sequences
        segment 4,21221=
        segment 6,17097=4646+3979+1000+292+388+2018+883+1731+753
        segment 8,14935=10609+3071
        12951+12976+13176+18393+13053+16047+14586+14172=11 5354 with > 90% of nucleotides
        in the coding regions available

        files bitse-r.GIF,bitse--r.GIF (not all available yet)
        bitse1r.GIF
        bitse2r.GIF
        bitse3r.GIF
        bitse5r.GIF
        bitse7r.GIF
        bitse81r.GIF
        bitse82r.GIF
        bitse47f.GIF
        bitse78r.GIF (for printing 7r,81r,82r on one sheet)

        (each of these has a subset of 900-1000 random,full(>90%),aligned sequences from that set,
        each line is one sequence,each row is one position with mutations, each black pixel is a difference
        from the average at that position. sequences and positions are resorted so to give minimum
        sum of neighbor differences ((approximately) solving the corresponding Traveling Salesman Problem))
        each set divides into an (mostly USA,Canada) American part and an East(EU,AS,AF,OZ) part
        which are identified by the common thick black vertical bars
        usually these are about the same size (except 81,82,47,45,69,...)
        Segment 3 has 2 American and 2 Eurasian parts.

        [I should add years and serotypes and amino-acid-sequences]


        { improvement ideas for the next updates:
        include amino-acids - bipartite , include years, serotypes
        include the 3499 Environment sequences, also humans, swine, etc
        who have avian-like-sequences (-->all human not H1N1,H3N2, all other
        than bat,human,swine,equine,canine , maybe exclude gull H13 ,
        separate America,Eurasian and one list for all the rest}
        Last edited by gsgs; March 17, 2015, 02:49 AM.
        I'm interested in expert panflu damage estimates
        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

        Comment

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