https://github.com/ship561/hts-exploration
Tip revision: f8df857b16bd813a881c68669053b85d5f9fbc29 authored by shermin on 04 January 2017, 19:23:06 UTC
Commit prior to submitting paper. Should be working. Need to add function to take in fasta/fastq data and calculate NCM enrichment.
Commit prior to submitting paper. Should be working. Need to add function to take in fasta/fastq data and calculate NCM enrichment.
Tip revision: f8df857
README.md
# hts-exploration
A Clojure library containing methods for analyzing HTS-SELEX data found in the SRA --- SRP077756
## Usage
The primary methods for analyzing the HTS reads for 2\_2 nucleotide cyclic motifs (NCM) is found in the analysis.context namespace. The function is calc-struct-features2 which takes the arguments stack-size, max gaps in current helix, sequence and structure tuple.
```clojure
;;; for the 2\_2 NCM, the number of base-pairs stacked is 2. The max bulge size is 3.
;;; The format of the data must be a sequence (s) and a structure tuple containing
;;; [structure free-energy] where the structure is represented in dot-bracket notation.
;;; This tuple is the structure line output from secondary structure prediction programs such
;;; as RNAfold
(calc-struct-features2 2 3 s [st nrg]); 2\_2 NCM, 3 base bulge/interior loop
(calc-struct-features2 3 3 s [st nrg]); 3\_3 NCM, 3 base bulge/interior loop
```
## License
Copyright © 2014 FIXME
Distributed under the Eclipse Public License either version 1.0 or (at
your option) any later version.
