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New Genome Comparator word size default.
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kjolley committed Apr 27, 2015
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Expand Up @@ -335,11 +335,11 @@ and speed.
sequence that the alignment has to cover in order to be considered (default:
50%).
* BLASTN word size - This is the length of the initial identical match that
BLAST requires before extending a match (default: 15). Increasing this value
BLAST requires before extending a match (default: 20). Increasing this value
improves speed at the expense of sensitivity. The default value gives good
results in most cases, but increasing this to 20 is almost as good (there was
1 difference among 2000 loci in a test run) and will speed up the analysis
approximately two-fold.
results in most cases. The default setting used to be 15 but the new default
of 20 is almost as good (there was 1 difference among 2000 loci in a test
run) but the analysis runs twice as fast.
* Use TBLASTX - This compares the six-frame translation of your nucleotide
query sequence against the six-frame translation of the contig sequences.
Sequences will be classed as identical if they result in the same translated
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