Blast a sequence with N's

0

Dear all

I'm blasting some sequences on nt database, on my local server.
My sequences are short (<100 bp) with this caracteristic:

seq 40N seq

Where seq ~28 bp

my command is the following:

blastn -task blastn-short -evalue 0.1 -qcov_hsp_perc 60 -word_size 7 -dust no -reward 2 -penalty -3 -gapopen 5 -gapextend 2 -query $FASTA -db nt

Blast don't found any match in the databses. But if i run the same command with the "-remote" option, i get back som site of interest. Someone know why this dfference? I revise my databse and it contains all of the founded sequences.

If the seq ~38 bp, and the size of the all sequence is more large than 100bp, blastn local found the same as remote running.

Someone can explian me what's the problem?

Regards!


sequence


blastn


Short

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