Fragrep: An Efficient Search Tool for Fragmented Patterns in Genomic Sequences

Lowe, 1997, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res., 25, 955, 10.1093/nar/25.5.0955 Macke, 2001, RNAMotif, an RNA secondary structure definition and search algorithm, Nucleic Acids Res., 29, 4724, 10.1093/nar/29.22.4724 Gautheret, 2001, Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles, J. Mol. Biol., 313, 1003, 10.1006/jmbi.2001.5102 Eddy, 2002, A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure, BMC Bioinformatics, 3, 18, 10.1186/1471-2105-3-18 Farris, 1999, Conserved features of Y RNAs revealed by automated phylogenetic secondary structure analysis, Nucleic Acids Res., 27, 1070, 10.1093/nar/27.4.1070 Teunissen, 2000, Conserved features of Y RNAs: a comparison of experimentally derived secondary structures, Nucleic Acids Res., 28, 610, 10.1093/nar/28.2.610 Kickhoefer, 2003, Identification of conserved vault RNA expression elements and a non-expressed mouse vault RNA gene, Gene, 309, 65, 10.1016/S0378-1119(03)00507-9 Segal, 2005, A discriminative model for identifying spatial cis-regulatory modules, J. Comput. Biol., 12, 822, 10.1089/cmb.2005.12.822 Jensen, 2004, BioOptimizer: a Bayesian scoring function approach to motif discovery, Bioinformatics, 20, 1557, 10.1093/bioinformatics/bth127 Bi, 2004, Bipartite pattern discovery by entropy minimization-based multiple local alignment, Nucleic Acids Res., 32, 4979, 10.1093/nar/gkh825 Aspegren, 2004, Novel non-coding RNAs in Dictyostelium discoideum and their expression during development, Nucleic Acids Res., 32, 4646, 10.1093/nar/gkh804 Kreppel, 2004, dictyBase: a new Dictyostelium discoideum genome database, Nucleic Acids Res., 32, D332, 10.1093/nar/gkh138