sequence/contig assembly

jenkins at aidsun.nibsc.ac.uk jenkins at aidsun.nibsc.ac.uk
Tue Mar 1 05:16:12 EST 1994




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In article <2kmef4$sis at overload.lbl.gov> bks at s27w007.pswfs.gov (Bradley K. Sherman) writes:

>>Could you describe this program in a little more detail?  Is this
>>a program to read gels?  Try to describe the program without
>>regard to what you think the limitations of the computer might be.

mhollowa at epo.som.sunysb.edu wrote

>I've always wanted something that would just make a meld between two or 
>three sequences at once and keep a simple line graphic of the accumulated 
>project.  Nothing too fancy.  It needn't be able to meld and sort 
>multiple sequences all at once and spit out alternate melds.  It would 
>have to be able to handle mismatches in the meld, of course, but again it 
>needn't be too fancy.  It can be a given that only very good data is 
>being used.  No ambiguity.  
>
>T>here have been times when I would have used such a program, even given 
>i>ts limitations, in preference to that frustrating set of powerful 
>programs in GCG.  Plenty of people are still writing sequence out on 
>pieces of paper and shuffling them around on their desk.
>
stuff deleted!

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There have been several notes recently concerning sequence assembly from all those sequenceing gels you have ran.

One of the best (if not the best) sequence assembly software comes in Roger Staden's package.  If you are a research institute, it's around a mere hundred pounds sterlimg, and it is excellent.  

If you have X-windows, its even better.

It is very simple, though can appear complicated to a non-computer user.

Unfortunately, I cant find his e-mail address.

I have now connection with Roger Staden except as a satisfied user of his package.

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              Adrian Jenkins
              jenkins at uk.ac.nibsc.computing  


"I think I'll write my tombstone - Here lies Edmund Blackadder, and he's
    bloody annoyed."
                                    Edmund Blackadder  BA IV 

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