dnapunctuation
The DNA Punctuation program searches for stem-loop structures in a DNA sequence
Danila Zaev, Anton Zaikin, Maria Poptsova
Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
COMPILLATION:
You can compile the program as easy as
g++ dnapunctuation.cpp -o dnapunctuation
To accelerate processing time one can try these parameters (essential when annotating large chromosomes):
g++ -O2 -march=native dnapunctuation.cpp -o dnapunctuation
Here, the executable version was compiled under Mac OS High Sierra, version 10.13.6
RUNNING:
The program takes 7 arguments:
- imput sequence file in fasta format
- Minimum size of a stem
- Maximum size of a stem
- Minimum size of a loop
- Maximum size of a loop
- Number of mismatches allowed
One should run the program as
./dnapuncutation L1.fna 6 15 3 10 1
where L1.fna is a sequence file containing L1 human transposon
6 is the minimum size of a stem 15 is the maximum size of a stem 3 is the minimum size of a loop 10 is the maximum size of a loop 1 is the number of gaps/mismatches allowed
The promram output is the text tab-delimitted file named according to the stem-loop parameters specified as input: L1.fna.S6-15_L3-10_M1.pal
L1.fna and L1.fna.S6-15_L3-10_M1.pal can be found in the main directory