g******1
发帖数: 295 | 1 For the following two sequences, I am doing blastn on Seq2 against Seq1
blastn -task blastn-short -outfmt "6 nident"
Seq1: ATTAGAWACCCBDGTAGTCC
Seq2: ATTAGATACCCTGGTAGTCC
The length of each sequence is 20. The blastn returns nident=17, with 3
mismatch.
However, T actually matches W and B, and G matches D.
With IUPAC characters, in this case, how can I also count ambiguous matches?
What I expect in this case is number of identity =20 instead of nident=17.
Is there any parameter for blastn so that I can get number of identity =20?
Thanks | y**********n
发帖数: 478 | 2 you can count the ambiguous matches yourself by a script based on the
alignment. | g******1
发帖数: 295 | 3 Doesn't blastn provide that output?
【在 y**********n 的大作中提到】
: you can count the ambiguous matches yourself by a script based on the
: alignment.
| y**********n
发帖数: 478 | 4 check the parameters bellow to see if you can get that output, otherwise you
need to make a script yourself.
http://www.molquest.com/help/2.3/programs/BlastN/parameters.htm
【在 g******1 的大作中提到】
: Doesn't blastn provide that output?
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