Any great tutorials on how to download sift/provean on your computer?

Question

[williamsbrian5064]

I've been trying to download sift/provean on my computer for the last week or so. I haven't had much luck with either of them. I've been trying to download the program on my mac and haven't had any luck. I figured that maybe the mac operating system wasn't ideal so I downloaded virtualbox so I could use ubuntu to try and use Linux. That seemed to work better but I'm still just not able to get either of them to work. I was just wondering if there were any better guides than the "install" instructions that come with the file? Maybe I just need to start posting the error messages and pray for the computer gods to help me?

Honestly any help would be amazing. I've dumped so much time in trying to download these programs and haven't really gotten anywhere.

[aka001]

What kind of errors did you get? Maybe you can post some of the errors?

[GenoMax]

If you are behind a firewall that is blocking the links/sites you are trying to reach then not much else is going to help short of doing the download from a different location or talking with your firewall admins.

[cpad0112]

If you are using ubuntu or mint, try

sudo apt-get install sift -y

Enable universe, multiverse, restricted repos and update the repos before you install sift, to be on safe side. Xenial (ubuntu) and Sonya (mint) have sift in their repos. Current version in repos is 4.0.3b

Answer 1

[h.mon]

I've dumped so much time in trying to download these programs and haven't really gotten anywhere.

You mean something like this didn't work?

wget http://sift.jcvi.org/www/sift4.0.3b.tar.gz
wget https://sourceforge.net/projects/provean/files/provean-1.1.5.tar.gz

Answer 2

[Ibrahim Tanyalcin]

Hi William,

If you need the polyphen2 and the sift scores for a list of proteins with either Ensembl ID, Uniprot ID or RefSeq, I would try the Ensembl Biomart. I use these for plotting these scores for my protein of interest. Here is sample video from my own work. In Biomart you are advisied to submit up to 500 protein IDs, but they also provide you a perl script which can fetch much more and cache the data on your computer.

Answer 3

[pfs]

Provean - http://provean.jcvi.org/downloads/README Polyphen2 - http://genetics.bwh.harvard.edu/pph2/dokuwiki/downloads