Exact match in blastn
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7.3 years ago
Whoknows ▴ 880

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 can not 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.

blastn blastall mismatch • 2.3k views
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7.3 years ago
edrezen ▴ 720

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'.

 

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7.3 years ago
Whoknows ▴ 880

thanks a lot for answer, i don't know what  'gwak'  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.,

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gawk is a tool that can perform simple treatments on text files. It is often distributed on Linux (or awk on macos)

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7.3 years ago
Daniel ★ 3.8k

You are better using something other than blast if you want to do exact matching. An example is this perl script: 

https://github.com/passdan/scriptdrop/blob/master/probe_specificity_test

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.

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