estimation of base accuracy and putting N instead of - in sequence files

Rifat Hamoudi rifat at icr.ac.uk
Mon Jul 28 12:30:54 EST 1997


Hi,

	Recently I had a problem with some sequences in that it was 
giving me a noisy sequence upto 150bp and then good sequence from 
150bp to 500bp. But the problem is that eba program clipped the whole 
sequence and excluded it from the database. How can I change the eba 
parameters so that it becomes more adaptive, i.e. it looks at the 
sequence and if it is noisy at the beginning it will clip it and when 
it gets to good sequence it will leave it (include it) and then clips
the noisy bit at the end of the sequence instead of clipping 
everything as bad sequence.

Also, why does Staden change the Ns in the sequence to -  Is there 
anyway I can leave the Ns in the sequence, because when I blast the 
sequences the BLAST software gives a warning about the - 

Thanks.

Rifat.


rifat at icr.ac.uk





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