Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Recent Methods for RNA Modeling Using Stochastic Context-Free Grammars
CPM '94 Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching
Local Similarity in RNA Secondary Structures
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Faster genome annotation of non-coding RNA families without loss of accuracy
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
The 2-Interval Pattern Matching Problems and Its Application to ncRNA Scanning
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Accelerated microRNA-precursor detection using the Smith-Waterman algorithm on FPGAs
GCCB'06 Proceedings of the 2006 international conference on Distributed, high-performance and grid computing in computational biology
PMFastR: a new approach to multiple RNA structure alignment
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Structural alignment of RNA with complex pseudoknot structure
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Mining characteristic relations bind to RNA secondary structures
IEEE Transactions on Information Technology in Biomedicine
Function Annotation for Pseudoknot Using Structure Similarity
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A Memory Efficient Method for Structure-Based RNA Multiple Alignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Memory Efficient Algorithms for Structural Alignment of RNAs with Pseudoknots
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Algorithms for pseudoknot classification
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Local structural alignment of RNA with affine gap model
ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications
Structural alignment of pseudoknotted RNA
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
Designing Filters for Fast-Known NcRNA Identification
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
An Efficient Alignment Algorithm for Searching Simple Pseudoknots over Long Genomic Sequence
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Mining Featured Patterns of MiRNA Interaction Based on Sequence and Structure Similarity
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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The discovery of novel noncoding RNAs has been among the most exciting recent developments in biology. It has been hypothesized that there is, in fact, an abundance of functional noncoding RNAs (ncRNAs) with various catalytic and regulatory functions. However, the inherent signal for ncRNA is weaker than the signal for protein coding genes, making these harder to identify. We consider the following problem: Given an RNA sequence with a known secondary structure, efficiently detect all structural homologs in a genomic database by computing the sequence and structure similarity to the query. Our approach, based on structural filters that eliminate a large portion of the database while retaining the true homologs, allows us to search a typical bacterial genome in minutes on a standard PC. The results are two orders of magnitude better than the currently available software for the problem. We applied FastR to the discovery of novel riboswitches, which are a class of RNA domains found in the untranslated regions. They are of interest because they regulate metabolite synthesis by directly binding metabolites. We searched all available eubacterial and archaeal genomes for riboswitches from purine, lysine, thiamin, and riboflavin subfamilies. Our results point to a number of novel candidates for each of these subfamilies and include genomes that were not known to contain riboswitches.