One of our users searched a primer against a databank and could not
retrieve the sequence for which the primer was optimized. The
reason turned out to be that :
the sequence is ACNACNAGGTCNCCRTCYTTGATGAT
fasta against the sequence vi:U44402 yields :
SCORES Init1: 32 Initn: 32 Opt: 88
80.8% identity in 26 bp overlap
19 9
gbvca1 ATCATCAARGAYGGNGACCTNGTNGT
||||||||:||:||:|||||:||:||
u44402 ATTGCCTATTATAGGGGTAAAGACAGTTCTATCATCAAGGATGGGGACCTGGTGGTCTGT
4400 4410 4420 4430 4440 4450
while fasta against vi:HG25543 yields :
SCORES Init1: 80 Initn: 80 Opt: 88
80.8% identity in 26 bp overlap
19 9
gbvca1 ATCATCAARGAYGGNGACCTNGTNGT
||||||||:||:||:|||||:||:||
hg2554 ATTGCTTATTATAGGGGCAAAGACAGTTCCATCATCAAGGACGGAGACCTAGTGGTGTGC
120 130 140 150 160 170
The sequence vi:U44402 is evidently not found because its Initn score
is lower than the Initn score of vi:HG25543 and many other sequences
and thus sinks so far away in the list of hits that you do not look
at it. But how is it possible that identical alignments are scored
so differently ?
Guy Bottu
