ESTBlast

ilyas m khan khan at hollywood.u-net.com
Tue Jul 22 19:12:21 EST 1997


First thing: don't worry about all that computer jargon, crap about
accession numbers, vaxs, passwords etc, etc, etc.

Second thing: you seem to have internet access, this is a much easier
relatively painless way of accessing the Genbank database. There are two
ways of doing this, first through Pedro's page, go to any search engine
and enter 'pedro molecular biology' and you should be directed to this web
site. then you just scroll down until you come to blast search blastn for
nucleotide, blastx for a protein search of your gene sequence, although it
sounds as if you need blastn. I reccomend you use Genbank search at NCBI.
The genbank search at NCBI (and at other centers) is basically
interactive, you can paste your sequence in a box, choose which database
you wish to search, the default genbank nucleotide database or you can
choose the EST database which is called dBEST, and finally you choose what
type of search you want to do, the default setting is blastn, which is as
you probably already know search of a nucleotide sequence. Then its a
simple dab of the mouse button when the cursor is on the SEARCH box and
just let the internet do the rest.

Third thing: the output you recieve will be a number of homologous
sequences, all of which can be directly accessed, (no accession number
needed, hooray), and the sequences are usually quite good, sometimes over
500bp, although beware many haven't been formatted so that there will be
lots of N's in the sequence and 5' and 3' sequence tends to be a tad
dodgy. You can either cut and paste the sequence out or save the file
directly onto your harddrive.

Fourth point: you will need to stitch your sequences together, and if you
haven't got a piece of software, there is a free program which can do this
for you, its called MACAW (as in the bird) and it works a treat (may be
able to email across although its quite large)!

I've used all the techniques above to do essentially what you hope to do,
after using the programs for a while you will beome a Genbank guru, and
people will undoubtidly come to you for advice. if you have any problems,
feel free to email



                                          ilyas



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