Hi, thanks a lot!
However, what I would need is an option to run perc_identity without considering gap positions. For example, if I do -perc_identity 100, I want blastn to pick the alignment
ATCGATCGAGGGG
ATCGAT--AGGGG
but perhaps there is no such an option available.
Many thanks!
-
You could try to set -gapopen and -gapextend to "0". I'm not so sure it will change the % identity value though..Leave a comment:
-
blastn perc_identity on matching region
Hi,
I am using blastn with the -perc_identity option. That way, blastn discards the alignments which do not fulfil a minimum % identities. However, I've just noticed that this option takes into account the gap positions and I would need it doesn't. For example, I would need these 2 sequences to yield an identity of 100%. Is that possible?
ATCGATCGAGGGG
ATCGAT--AGGGG
Many thanks!
-
The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM
Leave a comment: