RNAshapes: an integrated RNA analysis package based on abstract shapes

被引：222

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

页码：500 / 503

页数：4

共 12 条

[1] A statistical sampling algorithm for RNA secondary structure prediction
Ding, Y
Lawrence, CE
[J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (24) : 7280 - 7301
[2] A comprehensive comparison of comparative RNA structure prediction approaches
Gardner, PP
Giegerich, R
[J]. BMC BIOINFORMATICS, 2004, 5 (1)
[3] Abstract shapes of RNA
Giegerich, R
Voss, B
Rehmsmeier, M
[J]. NUCLEIC ACIDS RESEARCH, 2004, 32 (16) : 4843 - 4851
[4] Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%
Havgaard, JH
Lyngso, RB
Stormo, GD
Gorodkin, J
[J]. BIOINFORMATICS, 2005, 21 (09) : 1815 - 1824
[5] FAST FOLDING AND COMPARISON OF RNA SECONDARY STRUCTURES
HOFACKER, IL
FONTANA, W
STADLER, PF
BONHOEFFER, LS
TACKER, M
SCHUSTER, P
[J]. MONATSHEFTE FUR CHEMIE, 1994, 125 (02): : 167 - 188
[6] Dynalign: An algorithm for finding the secondary structure common to two RNA sequences
Mathews, DH
Turner, DH
[J]. JOURNAL OF MOLECULAR BIOLOGY, 2002, 317 (02) : 191 - 203
[7] THE EQUILIBRIUM PARTITION-FUNCTION AND BASE PAIR BINDING PROBABILITIES FOR RNA SECONDARY STRUCTURE
MCCASKILL, JS
[J]. BIOPOLYMERS, 1990, 29 (6-7) : 1105 - 1119
[8] Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction
Reeder, J
Giegerich, R
[J]. BIOINFORMATICS, 2005, 21 (17) : 3516 - 3523
[9] SIMULTANEOUS SOLUTION OF THE RNA FOLDING, ALIGNMENT AND PROTOSEQUENCE PROBLEMS
SANKOFF, D
[J]. SIAM JOURNAL ON APPLIED MATHEMATICS, 1985, 45 (05) : 810 - 825
[10] SHAPIRO BA, 1988, COMPUT APPL BIOSCI, V4, P387

← 1 2 →