Sequence alignment

Duncan Clark Duncan at genesys.demon.co.uk
Wed Jun 8 05:00:42 EST 1994


Hi Folks,

I'm stuck again!

I want to align 3 sequences of roughly 3kb with a 2.5kb gene somewhere in 
each. The aa homolgy is of the order of >90% and DNA>70% but can I get 
ClustalV or Macaw to do it? No chance. ClustalV hangs halfway through whilst
Macaw gradually over an hour or two at least appears to be getting somewhere.
Microgenie will align two of the three (in seconds) but cannot do three at
once. I'm running a 66Mhz 486 with 20Mb RAM, Macaw under Win3.1. I know 
ClustalIV used to fall down on DNA sequences longer than approx. 700bp but
I thought that was fixed. Both Macaw and ClustalV align the aa sequences 
without problems (and fast). I don't really wnat to split thes equences up
into 700bp chunks then stick the sunsequent alignment back together again. Am
I asking too much?

Are there any alternatives/pointers. I only do alignments once in a blue moon
so I can't really justify any commercial package. Conrad and Mount and Oligo2
do all my routine analysis fine.

Many thanks

Duncan   

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Duncan Clark                        | Internet:    duncan at genesys.demon.co.uk
GeneSys Ltd.                        | Compuserve:  100015.1406 at compuserve.com
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