scholarly journals RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

2015 ◽  
Vol 43 (W1) ◽  
pp. W507-W512 ◽  
Author(s):  
Matan Drory Retwitzer ◽  
Maya Polishchuk ◽  
Elena Churkin ◽  
Ilona Kifer ◽  
Zohar Yakhini ◽  
...  
Keyword(s):  
Pattern Matching ◽  
Web Server ◽  
Sequence Structure ◽  
Rna Sequence ◽  
Motif Detection

scholarly journals SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

2014 ◽  
Vol 42 (W1) ◽  
pp. W356-W360 ◽  
Author(s):  
Paolo Di Tommaso ◽  
Giovanni Bussotti ◽  
Carsten Kemena ◽  
Emidio Capriotti ◽  
Maria Chatzou ◽  
...  
Keyword(s):  
Web Server ◽  
Rna Sequence ◽  
Multiple Alignments

scholarly journals RASS: a web server for RNA alignment in the joint sequence-structure space

2014 ◽  
Vol 42 (W1) ◽  
pp. W377-W381 ◽  
Author(s):  
Gewen He ◽  
Albert Steppi ◽  
Jose Laborde ◽  
Anuj Srivastava ◽  
Peixiang Zhao ◽  
...  
Keyword(s):  
Web Server ◽  
Sequence Structure ◽  
Structure Space

scholarly journals A heuristic approach for detecting RNA H-type pseudoknots

2005 ◽  
Vol 21 (17) ◽  
pp. 3501-3508 ◽  
Author(s):  
Chun-Hsiang Huang ◽  
Chin Lung Lu ◽  
Hsien-Tai Chiu
Keyword(s):  
Web Server ◽  
Heuristic Approach ◽  
Biological Processes ◽  
Rna Structures ◽  
Online Analysis ◽  
Rna Sequence ◽  
Associated Functions ◽  
Almost All ◽  
The Web

Abstract Motivation RNA H-type pseudoknots are ubiquitous pseudoknots that are found in almost all classes of RNA and thought to play very important roles in a variety of biological processes. Detection of these RNA H-type pseudoknots can improve our understanding of RNA structures and their associated functions. However, the currently existing programs for detecting such RNA H-type pseudoknots are still time consuming and sometimes even ineffective. Therefore, efficient and effective tools for detecting the RNA H-type pseudoknots are needed. Results In this paper, we have adopted a heuristic approach to develop a novel tool, called HPknotter, for efficiently and accurately detecting H-type pseudoknots in an RNA sequence. In addition, we have demonstrated the applicability and effectiveness of HPknotter by testing on some sequences with known H-type pseudoknots. Our approach can be easily extended and applied to other classes of more general pseudoknots. Availability The web server of our HPknotter is available for online analysis at http://bioalgorithm.life.nctu.edu.tw/HPKNOTTER/ Contact [email protected], [email protected]

Analysis of RNA sequence structure maps by exhaustive enumeration II. Structures of neutral networks and shape space covering

1996 ◽  
Vol 127 (4) ◽  
pp. 375-389 ◽  
Author(s):  
W. Gr�ner ◽  
R. Giegerich ◽  
D. Strothmann ◽  
C. Reidys ◽  
J. Weber ◽  
...  
Keyword(s):  
Shape Space ◽  
Sequence Structure ◽  
Rna Sequence ◽  
Neutral Networks
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