<p>Hi All,</p>

<p>I am using blastn to blast my data against tRNAs which is extracted from RFam database. Then I picked one match from the blast result to confirm it by directly searching my read in RFam online (<a href='http://rfam.sanger.ac.uk/search'>http://rfam.sanger.ac.uk/search</a>).</p>

<p>Here is my read which have a 100% match with a tRNA:
CCCATTCTTGCGACCCGGGTTCGATTCCCGGGCGGCGC</p>

<p>This is the matched tRNA from RFam:
GCGCCGCTGGTGTAGTGGTATCATGCAAGATT<strong>CCCATTCTTGCGACCCGGGTTCGATTCCCGGGCGGCGC</strong>A</p>

<p>Clearly it's a perfect match (in bold). But when you search my query in RFam, there is no hit. However, the subject tRNA can be found in RFam.</p>

<p>Could anybody tell me what's the problem?</p>

<p>I think that it is because your tRNA sequence is truncated by having short reads. Covariance models use (among other things) information about the internal base-pairing of the RNA, in this case the cloverleaf structure.</p>

<p><img src='http://upload.wikimedia.org/wikipedia/commons/thumb/5/59/TRNA-Phe_yeast_en.svg/500px-TRNA-Phe_yeast_en.svg.png' alt='tRNA from Wikimedia commons' /></p>

<p>(By Yikrazuul (Own work) <a href='http://creativecommons.org/licenses/by-sa/3.0'>CC-BY-SA-3.0</a>, via Wikimedia Commons) </p>

<p>If you imagine an extreme case, where your tRNA fragment is exactly divided in half (this is almost the case for your example!), or you by chance get only a large part of the variable loop, then you
see that you loose a large portion of the most significant base pairing (acceptor stem, anticodon loop+ stem). That will possibly drop the score immediately, 
because the structure left would be a single hairpin loop, which are quite frequent and not significant for a tRNA. That means that for truncated sequences, blast might be more sensitive than RFam or tRNAscan-SE.</p>
