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How to Research Sequences

W

wetDirt

Senior Moderator
More info on the H5N2 vaccine:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?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?
 
Re: H5N1 Sequence From Egypt

Re: H5N1 Sequence From Egypt

wetDirt said:
More info on the H5N2 vaccine:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?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?
Click to expand...

Flu sequences at GenBank are list alphabetically within each serotype here

http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=11320&lvl=3&keep=1&srchmode=1&unlock

H5N2 is here

http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=119220&lvl=3&lin=f&keep=1&srchmode=1&unlock

ck/Hidalgo/232/94 is here

http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=260000&lvl=3&lin=f&keep=1&srchmode=1&unlock

each gene is here

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=Search&dopt=DocSum&term=txid260000[Organism:noexp]
 
Re: H5N1 Sequence From Egypt

Re: H5N1 Sequence From Egypt

wetDirt said:
More info on the H5N2 vaccine:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?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?
Click to expand...
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.html?action=search&form_page=zilch&seg=any&hspecies=Any&text=Hidalgo&field=ALL&viewas=slist&orderby=datedes&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>
 
Re: How to Research Sequences

Here is the BLAST website:

http://www.ncbi.nlm.nih.gov/BLAST/B...HTTPGET=Yes&SHOW_LINKOUT=yes&GET_SEQUENCE=yes

Here is how to work it:
Niman said:
Easiest to see if you select "query anchored with identities" for the alignment view.
Click to expand...

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.
 
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