EST databases

Bill_A_Nussbaumer at ms.bd.com Bill_A_Nussbaumer at ms.bd.com
Thu Feb 3 15:59:33 EST 2000





Bill A Nussbaumer at BDX
02/03/2000 03:58 PM

Hi,

I'm not sure how much help I can be so I was waiting to see if you received any
responses from someone more knowledgeable on the matter.  But you haven't yet,
as far as I've seen, so I'll at least put out an idea I had.  Keep in mind I've
never tried it.

First of all check out the pearl script "webblast" at
http://www.genet.sickkids.on.ca/bioinfo_resources/software.html <--- this might
do what you want.

Just save the script as a text file, rename it with a .pl extension and follow
the instructions in the commented areas before running.  I haven't yet gotten
through my firewall but I haven't tried very hard either.

To run it, of course, you'll need pearl.  If you are running UNIX then you
surely already have it but you can check with your sysadmin.  If your running a
Windows machine go here http://www.activestate.com/ to get active pearl for your
windows system.  It's very easy to install, just read the instructions.  If your
running Mac then look for a solution because I don't know how to run pearl on a
Mac.  I don't think webblast works on a Mac anyway.

If you find yourself needing to switch around a number of file format types on a
windows machine you may find this app handy --> Seqverter at
http://www.genestudio.com/  This will allow you to convert files from one format
to another relatively easy once you get a feel for the program (Watch out for
illegal file names due to | characters pulled from a fasta header.

The reason I mention this app (By the way it's a windows app) is because you may
find the fastest way to do multiple Blasts using webblast (I think it will do
this) is to obtain all of your sequences in fasta format.  If you already have
this then great.  If not the fastest way to do this might be to do a nucleotide
entrez search for your accession numbers at ncbi (i.e. search for "ab030734 OR
ab030733 OR ap001107" without the quotes and limiting the search to the
accession field will give you only those three entries).  You could then display
them in fasta format --> save as a text file --> import into clustalX (
http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html ) -->  save as an MSF
file ---> run the MSF file through Seqverter and you'll get each sequence in
it's own fatsa formatted file.  (Is that enough of a work around for you?  hehe)

Well, in the absence of another reply from someone more knowledgeable (I'm just
learning this stuff) you might want to give these ideas a look and see whether
or not they will solve your problem.

Hope it's of some help.

Bill Nussbaumer





Hi

I am currently using a DNA oligonucleotide microarray, many of the
oligonucleotide probe sequences are derived from mouse EST's. I am
looking for some method/database to be able to enter many EST accession
numbers and receive homology results or the relevant data to allow
identification of the EST's in large batches. Does anyone know a method
of doing this rather than the method i am currently using which involves
using Genbank at NCBI and entering each accession number individually to
obtain the sequence then performing a BLAST search? There must be a
quicker way.


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