<p>Hi all,</p>

<p>I have DNA sequencing data where human tumors have mouse reads as per the experiment protocol(similar to PDX).</p>

<p>I have calculated the read counts of these mouse genes. using HTSEQ-count,after this I want to select only those mouse genes which have no homology to the human genome and only mouse specific.</p>

<p>Is there any tool to do this besides BLAST?Let me know.</p>

<p>Thanks,</p>

<p>Ron</p>

<p>Find all the orthologous genes between the two species (one database of many <a href="http://www.informatics.jax.org/homology.shtml">here</a>, one how-to <a href="http://www.ensembl.info/blog/2009/01/21/how-to-get-all-the-orthologous-genes-between-two-species/">here</a>), the mouse genes not present in this list are the genes you want.</p>
