RNAshapes: an integrated RNA analysis package based on abstract shapes

被引：221
|
作者：
Steffen, P [1 ]
Voss, B
Rehmsmeier, M
Reeder, J
Giegerich, R
机构：
[1] Univ Bielefeld, Fac Technol, D-33594 Bielefeld, Germany
[2] Univ Bielefeld, Ctr Biotechnol, D-33594 Bielefeld, Germany
[3] Univ Freiburg, Inst Biol 2, D-79104 Freiburg, Germany
来源：
BIOINFORMATICS | 2006年 / 22卷 / 04期
关键词：
D O I：
10.1093/bioinformatics/btk010
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus shapes approach. This new package is completely reimplemented in C and outruns the original implementations significantly in runtime and memory requirements. Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching and a sliding window approach.
引用
收藏
页码：500 / 503
页数：4
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