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blastn not acknowledging "N" string.

My sequence of CCNCCNTNNCCNC does not show any results when I use it as input in blastn on the human genome, although I am a 100% sure that results should come up. Changing the "N" string with any other of the nucleotide strings does give valid results, so I suspect that the tool just doesn't work using the "N" string. Does anyone know how I can make sure that some results do come up?

blast blastn sequencing nih
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updated by Ram Ram • written by robbenstijn • robbenstijn

I don't think blastn is designed for such small degenerate sequence.

For short sequences, word-size must be less than half the query length, otherwise reliable hits can be missed.

Even ,when ignoring the CR/LF, a bunch of hits is found using a simple grep...

$ grep 'CC.CC.T..CC.C' hs37d5_all_chr.fasta | wc -l
117794
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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks Pierre, I am not really sure what you mean. In the browserversion of BLAST, it should show results right?

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written by robbenstijn • robbenstijn

If you can use short-blastn instead of megablast in the "browser version" (assuming blast.ncbi.nlm.nih.gov?) then it might work, but as Pierre says, it might be too short and degenerate.

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written by cschu181 cschu181

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