I think you have a problen either with the way you are inputting your data
or there is something seriously wrong with your version of FASTS3.
FASTS3 is specifically designed so that results don't depend on the order
sequences are entered, how are you inputing your data? FASTS3 requires a
header and separation of fragments with commas, ie:
>a header of some kind
FRAGMENT1,
FRAGMENT2,
FRAGMENT3
it will consider fragments in any possible order. I think the input format
is quite sensitive , you should include a header, don't forget the commas
and don't put a full stop or a comma at the end.
FASTS3 is the only way to search multiple sequences of unknown order, there
are no BLAST implementations that can do that. There are workarounds like
entering sequences separated by a number of X's but the result is order
dependent and the stastics are uninterpretable.
Good luck....Ken
>Dear all.
> This is for those that are always up-to-date with search
>algorithms.
>I was trying FastaS3 because it allows to put several sequences at the time,
>( for instance, sequences got from HPLC peaks ) but the results depends
>on the order you load the different peptides; that means that the
>program,when checking alignements, consider that the first peptide will be
>before than the second in the protein to be, and the second will be before
>than the third and so on. Of course, one does not know which is the real
>order, so ??.
> Meanwhile, another question. Is there other program, besides Blastp,
>allowing more that one sequence ?
> Any comments will be useful.
>Thanks in advance
> Susana L.
>
>********************************************
>Susana Linskens
>LANAIS-PRO
>Junin 956
>1113 Buenos Aires - ARGENTINA
>linskens@qb.ffyb.uba.ar
>FAX: 54-11-4508-3652
>Phone: 54-11-4508-3651
>********************************************
********************************
Ken I. Mitchelhill
The John Holt Protein Structure Laboratory
St. Vincent's Institute of Medical Research
41 Victoria Parade
Fitzroy 3065 Victoria
AUSTRALIA
Telephone: 61-3-9288 2480
Facsimile: 61-3-9416 2676
Email: k.mitchelhill@medicine.unimelb.edu.au
Laboratory: http://www.medstv.unimelb.edu.au/WWWDOCS/SVIMRdocs/JHPSL.html
ABRF: http://www.abrf.org
***********************************