PC sequence alignment program

Keith James kdj at fes6.sanger.ac.uk
Thu Feb 25 07:28:40 EST 1999

>>>>> "Yuri" == Yuri Trembath <tremby at GENETICS.UIOWA.EDU> writes:

    Yuri> Dear all, Sorry to raise a mildly ancient topic for some of
    Yuri> these newsgroups, but I'd be interested in hearing opinions
    Yuri> on any and all sequence alignment programs for
    Yuri> Windows95/98/NT PCs.  I'm looking for something that will
    Yuri> read ABI sequence files and allow me to do multiple
    Yuri> alignments and export consensus sequences for BLAST
    Yuri> searches.  Identification of restriction sites, exons,
    Yuri> repeats, ORFs, etc. would be bonus.  Cost comparisons would
    Yuri> also be appreciated.

If you want low cost/free for small numbers of sequences try Chromas
to view ABI traces (http://www.technelysium.com.au/chromas.html) and
then ClustalX for multiple alignments. You may find that ClustalX
reads ABI directly, but I've a feeling it doesn't.

Free for assembling lots of sequences (i.e. sequencing projects),
Phred/Phrap. You'll need a C compiler to build these. A colleague here
has built them on NT with Borland C++.

Low cost for doing the whole thing, Staden package. Used to be about
£100 for an academic licence. It's very well featured but you'll need
to run it via Exceed (or similar) from a Linux (or other Unix) box to
get it on your Windows PC.

Having said that, the cost of a new PC + Linux + Staden is lower than
the cost of a number of Windows sequence packages and has the
advantage that several Windows boxes can use it simultaneously.

Web searches will let you find any of the above. If there's one
package I would avoid, it's Lasergene by DNAStar as I think it has far
too many bugs for anything but occasional use (and I've used it
extensively, to my intense frustration!)


Keith James  --  kdj at sanger.ac.uk  --  http://www.sanger.ac.uk/Users/kdj
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA

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