Difficulty Getting Ncbi Vecscreen

Question

[jsporter]

Hi, I'm trying to get NCBI vecscreen (http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html) 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.

Does anyone know:

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

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.

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

Any help is appreciated.

[jsporter]

Is there a way to do vecscreen locally?

[jgibbons1]

Not that I am aware of.

[jsporter]

I figured out part (2): http://www.ncbi.nlm.nih.gov/books/NBK7167/

Answer 1

[jgibbons1]

You can download stand-alone-blast and the UniVec databases and then blast against UniVec locally. This will allow you to blast many sequences at once.

Answer 2

[rreid2]

This is a useful bit of info when running a local blast on UNIVEC vectors:

Their blast options!

blastn -reward 1 -penalty -5 -gapopen 3 -gapextend 3 -dust yes -soft_masking true -evalue 700 -searchsp 1750000000000

Described here: http://www.ncbi.nlm.nih.gov/tools/vecscreen/about/

Hope this helps someone out there. #TSANIGHTMARES