<p>Hi,
I'm trying to get NCBI vecscreen (<a href='http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html'>http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html</a>) to work as a command-line for examining many sequences.  I've tried compiling NCBI toolbox, but NCBI toolbox is very large and didn't work for me very well.  I tried compiling with only blast, but the dependencies for vecscreen don't seem to be included when I tried to run vecscreen.  I tried using qblast (with blastn) in BioPython with the parameters for vecscreen on the website, but I got different results.  I tried compiling NCBI toolbox on linux and windows.  I couldn't find how to compile blast, etc. in Visual C++ on Windows, and the linux attempt didn't have the dependencies or something for vecscreen.</p>

<p>Does anyone know:</p>

<ol>
<li>Can vecscreen be used in biopython somehow?  Maybe with qblast?</li>
<li>What configuration options, etc. do I need to run for the NCBI toolbox to get vecscreen to compile on windows or linux?</li>
</ol>

<p>The BioPython qblast parameters that I used are:
result_handle = NCBIWWW.qblast("blastn", "UniVec", record.seq, expect=700, filter="m D", nucl_penalty=-5, gapcosts="2 2", searchsp_eff=1.75e12)
VecScreen says that gapcosts should be "3 3", but qblast doesn't accept this.  I got different results than running vecscreen from the website.</p>

<p>The VecScreen parameters are pre-set using blastn options: 
-q -5 -G 3 -E 3 -F "m D" -e 700 -Y 1.75e12</p>

<p>Any help is appreciated.</p>

<p>You can  download <a href='http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download'>stand-alone-blast</a> and the <a href='ftp://ftp.ncbi.nih.gov/pub/UniVec/'>UniVec</a> databases and then blast against UniVec locally. This will allow you to blast many sequences at once. </p>
