Dear Netters:
I have tried to compare a degenerative oligonucleotide with the databases
using fasta. However checkeing the result I realize fasta can not
understand that ambiguitycodes can mean an identity not only a similarity.
see following example
SCORES Init1: 112 Initn: 112 Opt: 112
78.1% identity in 32 bp overlap
10 20 30
E1B-20 CARGARAANGTSATCAARACYTTRGATTTT
||:||:||:||:|||||:||:||:||||||
ad5001 TCTTTGAATCTGGGTCACCAGGCGCTTTTCCAAGAGAAGGTCATCAAGACTTTGGATTTT
1910 1920 1930 1940 1950 1960
E1B-20 TC
||
ad5001 TCCACACCGGGGCGCGCTGCGGCTGCTGTTGCTTTTTTGAGTTTTATAAAGGATAAATGG
1970 1980 1990 2000 2010 2020
In this comparison I would like the program to realize that the oligo
E1B-20 in fact is 100% homologous to tha ad5001 sequence.
Do anyone have any suggestion how this could be done with the gcg package
or any netservices?
Yours
BOSSE
