cpg_distribute as written by Tim Cutts and Gos Micklem
This directory contains the source code of a program written by Tim Cutts and Gos Micklem (in 2004) that detects CpG islands in nucleic acid sequences. The program is referenced in the Ensembl database, but is not available elsewhere to my knowledge.
The code provided in this commit was provided to me by Gos Micklem.
Usage:
./cpg -h
Usage: ./cpg [options] [file]
Options:
-h This message
-a .ace format output
-l nn length threshold
-g nn %GC threshold
-o nn observed/expected threshold
Stringent CpG island: -l 1000 -g 50 -o 0.6
* Sensible values to run are:
./cpg -l 400 -g50 -o0.6 14b7.seq
"acedb output":
./cpg -l 400 14b7.seq
EM:HS14B7 1950 2383 143 CpG:32 62.4 0.71
seqname start end score #_of_CpGs %GC observed/ expected ratio
Default output:
./cpg -al 400 14b7.seq
Feature Predicted_CpG_island 1950 2383 0.71 "Predicted CpG island: 62.4 %GC, o/e=0.71, #CpGs= 32"
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent