Detecting a stealth anthrax toxin gene The truth behind Blast
The DNA sequence must tell the story
The standard way of comparing the sequence against
others is to run the sequence through the non-redundant (NR) sequences
in GenBank, using the Blast
facility at NCBI. You do this,
and much to your surprise you get the result displayed by clicking
here. All you get are hits with E-values well above 1, clearly noise.
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sample DNA sequence
vs
toxin DNA sequence
... No similarity!
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This result doesn't make sense! This region of the
lef gene is highly conserved. If PCR picked up the fragment, then Blast should
pick up the sequence.
Maybe you've encountered a novel toxin sufficiently related to lef to permit PCR amplification, but not related enough to match known lef sequences in GenBank. This explanation doesn't sound very compelling, but you can think of no better at the moment, so you translate the DG47 sequence,
submit the translated sequence to Blast to search for similar proteins, getting the results displayed by clicking here.
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