Antwort: diffseq problems

[David.Bauer at SCHERING.DE]

Hello Obi,

these warnings only mean, that the emboss code which reads feature table
informations complains
about the /replace tag in variation.
But this was fixed in later releases. I don't get these warnings in 2.7.1.
Anyway, this should have no influence on the computation.
The two sequences you give as examples are genomic contigs of 185 and 100
kilobases.
Do you get any results out of diffseq?
If not, this could be due to memory limitations.
Emboss programs tend to do everything within physical RAM.
6 Gb on my machine is too small for this :-)

David.


2) I get the following errors:

Find differences (SNPs) between nearly identical sequences
Input sequence:AF129756
Second sequence:AP000504
Word size [10]: 2
Output report [1.diffseq]:
Warning: bad /replace value 'T'
Warning: bad /replace value 'C'
Warning: bad /replace value 'C'
Warning: bad /replace value 'T'
Warning: bad /replace value 'C'
Warning: bad /replace value 'GCCTT'

Any idea what's going on here?

Obi.