Announcement

Collapse
No announcement yet.

How to Research Sequences

Collapse
This is a sticky topic.
X
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • How to Research Sequences

    More info on the H5N2 vaccine:
    http://www.pubmedcentral.nih.gov/art...i?artid=446090
    J Virol. 2004 August; 78(15): 8372?8381.
    doi: 10.1128/JVI.78.15.8372-8381.2004.
    Copyright notice


    Effect of Vaccine Use in the Evolution of Mexican Lineage H5N2 Avian Influenza Virus
    Chang-Won Lee,1 Dennis A. Senne,2 and David L. Suarez1*

    The commercially available inactivated vaccines in Mexico all use the same seed strain provided by the Mexican government, designated A/CK/Mexico/232/94. The vaccine seed stock we received from NVSL was designated A/CK/Hidalgo/232/94.

    Just putting this here for my future reference. Dr Niman, how do I call up this sequence so I can play with BLAST?

  • #2
    Re: H5N1 Sequence From Egypt

    Originally posted by wetDirt
    More info on the H5N2 vaccine:
    http://www.pubmedcentral.nih.gov/art...i?artid=446090
    J Virol. 2004 August; 78(15): 8372?8381.
    doi: 10.1128/JVI.78.15.8372-8381.2004.
    Copyright notice


    Effect of Vaccine Use in the Evolution of Mexican Lineage H5N2 Avian Influenza Virus
    Chang-Won Lee,1 Dennis A. Senne,2 and David L. Suarez1*

    The commercially available inactivated vaccines in Mexico all use the same seed strain provided by the Mexican government, designated A/CK/Mexico/232/94. The vaccine seed stock we received from NVSL was designated A/CK/Hidalgo/232/94.

    Just putting this here for my future reference. Dr Niman, how do I call up this sequence so I can play with BLAST?
    Flu sequences at GenBank are list alphabetically within each serotype here

    http://www.ncbi.nlm.nih.gov/Taxonomy...hmode=1&unlock

    H5N2 is here

    http://www.ncbi.nlm.nih.gov/Taxonomy...hmode=1&unlock

    ck/Hidalgo/232/94 is here

    http://www.ncbi.nlm.nih.gov/Taxonomy...hmode=1&unlock

    each gene is here

    http://www.ncbi.nlm.nih.gov/entrez/q...erm=txid260000[Organism:noexp]

    Comment


    • #3
      Re: H5N1 Sequence From Egypt

      Thanks Henry.

      Comment


      • #4
        Re: H5N1 Sequence From Egypt

        Originally posted by wetDirt
        More info on the H5N2 vaccine:
        http://www.pubmedcentral.nih.gov/art...i?artid=446090
        J Virol. 2004 August; 78(15): 8372?8381.
        doi: 10.1128/JVI.78.15.8372-8381.2004.
        Copyright notice


        Effect of Vaccine Use in the Evolution of Mexican Lineage H5N2 Avian Influenza Virus
        Chang-Won Lee,1 Dennis A. Senne,2 and David L. Suarez1*

        The commercially available inactivated vaccines in Mexico all use the same seed strain provided by the Mexican government, designated A/CK/Mexico/232/94. The vaccine seed stock we received from NVSL was designated A/CK/Hidalgo/232/94.

        Just putting this here for my future reference. Dr Niman, how do I call up this sequence so I can play with BLAST?
        Sequences at Genabnk as well as those released by WHO are at the Los Alamos database.

        The search page is here

        http://flu.lanl.gov/search/

        You can search by hildago and get

        http://flu.lanl.gov/search/index.htm...atedes&num=500

        which includes

        <TABLE class=resultstable cellSpacing=0 cellPadding=4 width="100%" border=0><TBODY><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=64554 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>AY497136 </TD><TD>A/Chicken/Hidalgo/232/94 </TD><TD>MP (7) </TD><TD>985 </TD><TD>1994 </TD><TD>H5N2 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=64546 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>AY497128 </TD><TD>A/Chicken/Hidalgo/232/94 </TD><TD>NA (6) </TD><TD>1371 </TD><TD>1994 </TD><TD>H5N2 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=64538 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>AY497120 </TD><TD>A/Chicken/Hidalgo/232/94 </TD><TD>NP (5) </TD><TD>519 </TD><TD>1994 </TD><TD>H5N2 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=64562 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>AY497144 </TD><TD>A/Chicken/Hidalgo/232/94 </TD><TD>PA (3) </TD><TD>499 </TD><TD>1994 </TD><TD>H5N2 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=64522 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>AY497104 </TD><TD>A/Chicken/Hidalgo/232/94 </TD><TD>PB2 (1) </TD><TD>689 </TD><TD>1994 </TD><TD>H5N2 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=64530 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>AY497112 </TD><TD>A/Chicken/Hidalgo/232/94 </TD><TD>PB1 (2) </TD><TD>477 </TD><TD>1994 </TD><TD>H5N2 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=64481 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>AY497063 </TD><TD>A/chicken/Hidalgo/232/94 </TD><TD>HA (4) </TD><TD>996 </TD><TD>1994 </TD><TD>H5N2 </TD></TR></TBODY></TABLE>

        Comment


        • #5
          Re: How to Research Sequences

          Here is the BLAST website:

          http://www.ncbi.nlm.nih.gov/BLAST/Bl...T_SEQUENCE=yes

          Here is how to work it:
          Originally posted by Niman
          Easiest to see if you select "query anchored with identities" for the alignment view.
          So first you go to the sequences library, and locate the sequence you want. Once you find the sequence, and click on it, look in the upper-right-hand corner for the Proteins box. Click that to get to the sequence itself. Copy it to a text file, or keep the window open.

          Now select something to BLAST. Copy/paste that to the Blast window, select the formatting option described above, and wait impatiently for results.

          Comment


          • #6
            Re: How to Research Sequences

            here is an influenza-genome database
            http://www.flugenome.org/show_genomes.php

            they give 10,8,11,64,8,43,6,8 genotypes for the 8 segments.
            ~ 1billion theoretical combinations of which 259 occurred in practice in their database.
            16HAs,9NAs, and 2 NSs

            current H5N1 is all genotype (K,G,D,5J,F,1J,F,1E)
            I'm interested in expert panflu damage estimates
            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

            Comment

            Working...
            X