Wednesday, September 5, 2012

So RepeatScout is only going to serve as inspiration for a future mini-program. It doesn't do what I want it to and nothing else does either so I am going to use the same lines of thinking and make a simpler program. Also, I hate the command prompt of RepeatScout and every other program I am trying so that is the first thing that's going to change.

Now to clarify my line of thinking...

OBJECTIVE OF PROGRAM: To read a fasta sequence and find repetitive elements and note a degree of repetitiveness (# of repetitive elements? # of l-mers repeated? both? TBD). It will then sort the list of original fasta sequences by the degree of repetitiveness. Output will be a list of sorted fasta sequences (and maybe something else giving more details, we'll see).

Right now, RepeatScout is mostly written in C. I like C so I will probably continue to do so. Remember to add this paper to my Mendeley to remember exact details of RepeatScout algorithm.

Goal for the day: Write the file opener, reader, command prompt. Try to begin to incorporate l-mer finder.

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