sequence analysis software

Francis Ouellette francis at monod.biol.mcgill.ca
Thu Jun 18 10:33:47 EST 1992

  Reinhard Doelz (doelz at comp.bioz.unibas.ch)  writes:

>True. But a single system costs a fortune. You surely can buy a reasonable 
>PC for $5000. But, you don't buy the sequence database updates, and the 
>expertise how to use a system with it. And, you are sort of alone if you 
>need to reproduce results if you use standalone software. It sure is not 
>necessarily lethal nor desirable to go with the main stream, but do 
>you really spend time in evaluating 5 software packages in the PD, just 
>ending up in getting all of them because none does it all? 

I totally agree with you ...  and this is the selling pitch of all 
companies that sell these packages ... (do you work for any of 
them  ;-)

>Once you are talking about multiprocessor 486 I think you should ask your 
>nearest workstation sales rep and ask for the pricing. A mainframe package
>on a pizza box is presumably easier to maintain than a 8088 ported application
>on a 486 twin system. 

true again, but how many people are ready to make the jump, on their own?  
This is where departments have to think progressivelly and not depend 
on graduate students to run their sequence analysis facilities.  
Things like having a good workstation, good commercial package 
supplemented with the good PD stuff, and a person to look after 
that is not in the budget of all departments, or shall I say, 
not in the high priority of all departments!

>If you can make sure that 
>	(1) you can pay for the maintenance
>	(2) have some net expert on hand to get the workstation set up 
>	(3) get ONE REASONABLE (as opposed to all PD on any server) software
>that would be great. I think that a low-end Indigo, Sun or DECstation with 
>some GCG and a genome package from the PD would get you a good start 
>for about $25K. Surely beyond the $5K cited abouve but a real thing. 
>Now shop around and ask how long you can get a cpu usage with online 
>services for these $25K. Take your option. 

I fully agree again, and this is what the poeple at "YEAST CHI project"  have done (except they spent a bit more on the workstation :), and is definitelly the way to go, if you can afford it, and all of the group (not just the yeast CHI people) end up winners.

>Maybe some others in the same situation would like to speak up? 

yes, maybe they should ...


| B.F. Francis Ouellette  
| manager, yeast chromosome I project
| dept of biology, McGill university, Montreal, Qc, Canada
| francis at monod.biol.mcgill.ca

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