Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
tree: 10c988eec4

Fetching latest commit…

Cannot retrieve the latest commit at this time

..
Failed to load latest commit information.
src/findorf
test
.gitignore
README.md
project.clj

README.md

Clojure solution for BioStar code golf:

http://biostar.stackexchange.com/questions/5902/code-golf-finding-orf-and-corresponding-strand-in-a-dna-sequence

With a file of FASTA sequences, it prints the coordinates of the longest translation product for each sequence. All 6 frames are searched: forward and reverse in 3 frames.

It uses BioJava to handle FASTA parsing and translation:

http://www.biojava.org

and uses Leiningen to make the dependencies:

https://github.com/technomancy/leiningen#readme

Usage:

% lein deps
% lein run :findorf test.fa
t-1 [0 15 ONE]
t-2 [1 16 TWO]
t-3 [2 17 THREE]
t-r1 [0 15 REVERSED_ONE]
t-r2 [0 18 REVERSED_TWO]
t-r3 [0 15 REVERSED_THREE]
t-1-inner [3 21 ONE]
EX720612.1 [0 252 ONE]
Something went wrong with that request. Please try again.