Which is the MULTIPLE ALIGNMENT code that can be INTERFACED most EASILY ?

Mike Noren ev-michael at SPAMSTOPnrm.se
Thu Jul 31 16:12:38 EST 1997

x-no-archive: yes
Replying to (Georg Fuellen)

: a) the heuristic guide-tree driven alignment of 10-50 very short 
: (10-20 residues) biosequences,
: b) the alignment of 2 profiles (using a profile alignment like ClustalW
: does; again, the length is small),
: c) the optimal or near-optimal alignment of such sequences using sum-of-pairs.
: E.g., would you recommand ClustalW / MSA ? Or MAP ? Or MultAlin ?

I've tried ClustalW and Multalin of the ones you mention, and multalin
was so slow that I never got it to complete my alignment. Your
alignment is a _lot_ smaller than mine, so you could download ClustalW
1.6 and the freely distributable version of Multalin and try for
ClustalW 1.6 usually does an acceptable job, even with sequences rich
in gaps. With sequences of very different lengths it tends to fail
miserably, though, and I'm not sure how it'll handle very small
sequences like yours. Profile alignment usually works in v1.6, which
was not the case in v1.5.

ClustalW has the features you want, ie being guide-tree driven, and
its reasonably easy to use and accepts many file formats, which is a
welcome change. Since it is free I suggest you try it.
As an aside the PowerPC (Mac) version is several times faster than the
PC version for some reason - so much so that it's worth considering if
your alignment takes time.

: Any other tools you tried ?

SeqPup: Avoid at all cost until the programmer has got the program
past pre-alpha stage, so that it can actually do something without
Macaw: Same as above.

Also various sites which offer alignment on the net. You could shop
around for sites like that, and try their engines.

: Georg Fuellen

Michael Norén, Doctoral student,         Tel: Int +46 (0)8 6664236
Swedish Museum of Natural History,       Fax: Int +46 (0)8 666
Dept. of Invertebrate Zoology
P.O.B. 50007
S-104 05 Stockholm, Sweden


Silly Peter Nyikos quote of the day:
"You, the dogmatic scientism-ist, are the one who has been fighting
against the merest suggestion of even ordinary alien intelligences
being involved in the design of early earth microorganisms."
 -- Peter Nyikos to Howard Hershey, talk.origins, 97-07-28.

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