Closing Remarks - EvidentialGene Part 3

    It's been more than half a year since my last post. I wanted to make an update, but I lost interest in the project, and school was getting in the way. I decided I'd wait till most of my final exams were through and then finally post again. By that point, I'd lost the final genome produced by the EvidentialGene software that I had gotten to work as well as the images that went along with that process. I was switching my PC over from Ubuntu to Windows and had the file backed up to a USB I've since lost.

    Now, in the last post, I said that I'd outline the process of obtaining the proprietary software needed to run the pipeline. I still have some notes from that time, and in the rest of this post, I'm going to do my best to recall anything of importance.

fastanrdb -

• I don't have fastanrdb anymore or remember what files it came with since I misplaced the USB
• The links provided also no longer work from when I used them
• The link below is all I really know of that mentions exonerate or fastanrdb
• https://github.com/nathanweeks/exonerate/blob/master/src/util/fastanrdb.c

cd-hit -

• I used the link provided from the about page:
• https://github.com/weizhongli/cdhit/releases
• I remember having no luck with the new releases
• I can't recall anymore which exact release worked for me, but I know it wasn't any of the ones above V4.6.4
• Once you've downloaded the main file, look for a specific cd-hit program file, which you should just drag into the file you're using for the genome addition with evigene and other proprietary software

blastn and makeblastdb -

• This one is pretty self-explanatory and is a well-known software
• I just went to the NCBI BLAST website and downloaded what I needed
• https://blast.ncbi.nlm.nih.gov/

    I know the info is pretty vague here, and I don't even have the final genome anymore, but it's been a long while since I covered this project, and my interests have changed. School's out now, though, which means I'll have more posts coming soon. I'm working on a homemade capacitor, which is just gonna be a small part of another big project I've planned!