BLAST or BLAST-like software for Windows

reithm at imb.lan.nrc.ca MichaelE.Reith
Fri Dec 2 08:34:45 EST 1994

valeryt at ag.arizona.edu (Valery Thompson) wrote:
> I am looking for some software to perform BLAST searches that I can run 
> directly from my PC.  I have tried the network version available from NCBI and 
> find it very cumbersome to use particularly since it is a DOS only program
> and I have to not only exit Windows, but also unload my Windows network
> driver in order to use it.  I have a demo copy of WinGenie which has 
> several nice programs for sequence searching and sequence alignment,
> but requires me to send the requests by email.
> Is there anything available that combines the abilities of these two programs?
> Any input would be appreciated.
> Valery Thompson
> Muscle Biology Group
> University of Arizona

The WWW/Mosaic search by way of NCBI is a good one, although I find it
cumbersome to save the results of these searches.  Another alternative
is to multiplex your packet driver so as to be able to run Windows and 
DOS software simultaneously.  Pktmux (at boombox.micro.umn.edu in 
/pub/pc/packet-drivers/drivers) does this nicely.  The relevant lines 
of my autoexec.bat are:

pktdrv 60
pktdrv 61

ODIPKT loads the packet driver at interrupt 0x63, pktmux multiplexes
it twice (the default) at 0x60 and 0x61 - pktdrv statements.  Winpkt
is then loaded at 0x61 so that BLAST can use the packet driver at 
0x60, which it requires.  In Windows, make sure to set TCPMAN 
(assuming you're using Trumpet winsock) to use the packet driver at 
0x61.  You can then open a DOS window within Windows and run the BLAST 
software in it.  I've set up a batch file to run multiple searches one 
after the other, using the same set of parameters.  I find this the
most convenient way to do lots of searches at one time.  

Mike Reith
Marine Biology
NRC Institute for Marine Biosciences
reithm at imb.lan.nrc.ca

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