Protein-Accession-Google link ?
Frank Potthast Detectorvision AG
method which automatically
pulls information for that protein from the web ?
What can be done easily is something like
http://www.google.com/search?q=P19938
Or, if you know that the Accession is from swissprot, you could say
http://www.expasy.ch/uniprot/P19938
But you need to know it is swissprot ...
It would be nice to have a method like
http://www.google.com/protein?Accession=P19936&format=xml
(This example will not work, it is an illustration)
Anybody knows a method like that ?
Thank in advance from Switzerland ... Frank
Tim Hawkins
<frank.potth...@detectorvision.com> wrote:
} Given an Accession key of a protein, e.g. "P19938", is there any
} method which automatically
} pulls information for that protein from the web ?
}
}
} Or, if you know that the Accession is from swissprot, you could sayhttp://www.expasy.ch/uniprot/P19938
} But you need to know it is swissprot ...
}
} (This example will not work, it is an illustration)
}
} Anybody knows a method like that ?
}
} Thank in advance from Switzerland ... Frank
You may want to take a look at the program General Protein Mass
Analysis for Windows (GPMAW). They are not only compatible with SWISS-
PROT, but others as well.
SWISS-PROT and PIR are both available on the web. SWISS-PROT has to be
converted to FastA format before use (use DBindex).
SPTREMBL: Autotranslated nucleotide sequences from EMBL that differ
significantly from SWISS-PROT (and each other).
GenPept: Autotranslated database based on GenBank (from NCBI).
OWL: A combined database based on SWISS-PROT expanded with sequences
from PIR, autotranslated EMBL and others.
NCBInr: Like OWL it is a combined database. Unlike OWL it is updated
almost daily and contains considerably more sequence. However, the
redundancy is not quite as stringent so you are likely to end up with
a large number of (almost) identical sequences. Before you can use
this database for GPMAW, you have to convert it using the DBindex
utility.
DBnr: This is another frequently updated non-redundant database
availble through the EMBL-Heidelberg FTP server. From version 3.14
GPMAW is optimized to use this database. Like NCBInr it uses a
slightly non-standard form of the FastA format and has to be converted
with the DBindex utility.
GPMAW works with all of these, as it has the conversion utility
included.
Version 8.0, released in December, supports the X! Tandem ms/ms search
engine.
A demo program of an earlier release is available, and on-line
ordering can be done by going to http://www.chemsw.com/16006.htm
Good luck,
Tim Hawkins
Peter Hunziker
} Given an Accession key of a protein, e.g. "P19938", is there any
} method which automatically
} pulls information for that protein from the web ?
}
} What can be done easily is something like
} http://www.google.com/search?q=P19938
}
} Or, if you know that the Accession is from swissprot, you could say
} http://www.expasy.ch/uniprot/P19938
} But you need to know it is swissprot ...
}
} It would be nice to have a method like
} http://www.google.com/protein?Accession=P19936&format=xml
} (This example will not work, it is an illustration)
}
} Anybody knows a method like that ?
}
} Thank in advance from Switzerland ... Frank
}
}
Have you tried http://www.ebi.ac.uk/
Works with a variaty of different acquisition numbers from UniRef,
NCBInr,...
Best regards
Peter