I've got a couple of projects that have been sitting around because the genomics input needs cleaned up and made into a nice concise FASTA and that stuff is
Almost all of the things require you to concisely type the exact letters into boxes where there are no pictures. As you might have noticed, I get my letters mixed up when I type and that's exactly what you shouldn't do at consoles and command lines.
What if you could just click around a really simple GUI and DO ALL THE THINGS?
Hi, SEDA, (SEquence DAtabase builder) nice to meet you!
While you should read the paper, this software is super intuitive and really easy to use and you can get it for Windows or Penguins or whatever all here.
If you've got a huge FASTA file you'll either want to turn off the in memory indexing or figure out where it hides the Java limits for allowable RAM usage. I found instructions on where to find that text file for Penguin operating systems, but I can't hunt it down for Windows. I just turned it off for a 2GB file and let it do the work off the solid state drive. I don't know how long it took, I went to look for mass spec that was last seen leaving Memphis on Tuesday. It is amazing how often 1,400 pound (635 kg) things seem to end up in the wrong states. You'd think it would be more efficient to take it directly to the correct state, but I'm clearly no cartographer.
Best parts here, you can easily 6-frame translate and remove all your redundancy all within this program. Do you know that your organism absolutely definitely doesn't use some specific start codons? You can toss those out before you even get started. These are all things you can totally do in a console or at a command line, but I've never seen in a simple and easy to install GUI.
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