kelvintao / inverted-reapts-finder

Searching all the Inverted Repeats by local dynamic programming in the DNA sequences.

Inverted-Reapts-finder_DNA

Searching all the inverted repeats in the DNA sequences starting with 6 consecutive matched characters.

Main Function Details

IRfinderAll.m is an demo for how to use Inverted Repeats finder in the DNA sequence.
IRFinderS.m is an ready-made function for use.
findIRiniS.m is an main function for IR.
IRCodlocDyMatc.m is an locally dynamic function for sequence alignment.

Small Functions

outputSum.m and outputSumNoZero.m for summary of IR searching results.
scale6.m and reverScale6.m for consecutive 6 DNA characters to numbers for initial searching.
lettercmp for judging whether the two characters are one pair of A-T and C-G.
convert.m for an DNA character to a number.
lastClear.m for keeping only one searching result of the same ones.

Citation

Masters' Dissertation:
陶现明, 四核苷酸重复序列恒温扩增特性及基因组中反向重复序列特点的研究, **海洋大学, 2014.
Tao Xianming. The study on the isothermal amplification characteristics of tetranucleotide repeats and the features of inverted repeats in genomes, Ocean University of China,2014.
http://cdmd.cnki.com.cn/Article/CDMD-10423-1014368715.htm