in reply to Getting data from NCBI

Becky, NCBI switched over to a web service model years ago. Check out their eutils page for more info. If you do a lot of work with their data, I would recommend signing up on their mailing list.

For this particular query I think you would need to make an esearch request and then an efetch (but the folks at NCBI would now better): 

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/search.fcgi?db=protein&te
+rm=148261691&rettype=uilist&usehistory=y

[download]
and then using the info from esearch (basically WebEnv and query_key): 
 
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&We
+bEnv=<xxx>&query_key=<yyy>&rettype=fasta&retmode=xml&sort=pub+date

[download]

-derby

Update: The NCBI folks may have a better way of *directly* pulling the data based on ids -- I only query pubmed and the app normally has to do a search first so this search/fetch approach always worked well for me.

Update: Well ... it looks like you can directly pull: 

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id
+=148261691&rettype=fasta

[download]
Like I said, I really like what the NCBI folks are doing.

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Re^2: Getting data from NCBI
by jpearl (Scribe) on Apr 30, 2009 at 17:34 UTC
    I actually had a java program that did something very similar to this. It was very nice to just have the sequence as a string to read in, no parsing required! You can get the bare fasta formated sequence pretty easily if you use something like this: 

    my $giNum  = 148261691
my $seq    = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protei
+n&qty=1&c_start=1&list_uids="
.$giNum
."&uids=&dopt=fasta&dispmax=5&sendto=t&from=begin&to=end";

    [download]


    and then do something similar to what you're doing above.

    good luck!
[reply]
[d/l]
Re^2: Getting data from NCBI
by Becky (Beadle) on Apr 30, 2009 at 12:49 UTC
    You're a star, thanks! I never knew about that stuff before but will use it from now on! Becky
[reply]

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