Hi
I've used blastall to discover known miRNA for my small reads, my parameters were
blastall -p blastn -F F -e 0.01
but my problem is I cannot fix to find exact match, it found some target sequence but not they have not same length and some of them has mismatch,
Is there a way to determine prefect/exact match for blast or no?
Thanks friends.
Hi,
If the tabular output format of blast is enough for you, you can try the following
blastall -p blastn -F F -e 0.01 -d bank -i query -m8 | gawk '{if(index($3,"100.0")>0) { print $0}}'
It will keep aligments with only 100% of identity.
Note: you may have to use 'awk' if you don't have 'gawk'.
Thanks a lot for answer, I don't know what 'gawk' is, but sometimes you have 100% similarity but just a part of query is consider with the target sequence I mean:
Query : 21 nt
Target : 25 nt
Exact matched : Query (1,18) with 100% similarity
I want to find those sequences with same length and also without mismatch.,
You are better using something other than blast if you want to do exact matching. An example is this perl script
USAGE:
./probe_specificity_test test_file.fasta probe_seq outfile.txt
Something like:
./probe_specificity_test my_mirna.fasta CATGCATCGATGCATCGTA matching_sequences.txt
That will do gapped matching too so you would need to cut that bit out. It's also IUPAC compliant.
Hope this helps.
Log in to answer this question.
