Fine-grained parallel RNA secondary structure prediction using SCFGs on FPGA
Parallel Computing
Semantics and Ambiguity of Stochastic RNA Family Models
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
RNApasta: a tool for analysis of RNA structural alignments
International Journal of Bioinformatics Research and Applications
TRFolder: computational prediction of novel telomerase RNA structures in yeast genomes
International Journal of Bioinformatics Research and Applications
Bellman's GAP: a declarative language for dynamic programming
Proceedings of the 13th international ACM SIGPLAN symposium on Principles and practices of declarative programming
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
CRiSPy-CUDA: computing species richness in 16S rRNA pyrosequencing datasets with CUDA
PRIB'11 Proceedings of the 6th IAPR international conference on Pattern recognition in bioinformatics
Designing Filters for Fast-Known NcRNA Identification
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Accelerating ncRNA homology search with FPGAs
Proceedings of the ACM/SIGDA international symposium on Field programmable gate arrays
Chain-RNA: A Comparative ncRNA Search Tool Based on the Two-Dimensional Chain Algorithm
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Summary:infernal builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence-and structure-based multiple sequence alignments. Availability: Source code, documentation and benchmark downloadable from http://infernal.janelia.org. infernal is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X. Contact: nawrockie,kolbed,eddys@janelia.hhmi.org