Abstract

Background: Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N³) in memory. This is only practical for small RNAs. Results:...

Citations

3377	Introduction to Automata Theory Languages and Computation. 2nd edition. Addison-Wesley Publishing Company, 2000. de - Hopcroft, Ullman - 2004
996	A general method applicable to the search for similarities in the amino acid sequence of two proteins - Needleman, Wunsch - 1970
517	SR: Profile hidden Markov models - Eddy - 1998
509	Henikoff J: Amino acid substitution matrices from protein blocks - Henikoff - 1992
461	The Pfam protein families database - Bateman, Coin, et al. - 2004
436	Hidden Markov models in computational biology. Applications to protein modeling - Krogh, Brown, et al. - 1994
216	A Linear Space Algorithm for Computing Maximal Common Subexpressions[J - Hirschberg
174	RNA sequence analysis using covariance models - Eddy, Durbin - 1994
157	Simultaneous solution of the RNA folding, alignment and protosequence problems - Sankoff - 1985
130	W: Optimal alignments in linear space - EW, Miller - 1988
115	Comparing multiple RNA secondary structures using tree comparisons - Shapiro, Zhang - 1990
83	An efficient recognition and syntax algorithm for contextfree algorithms - Kasami - 1965
68	The Ribonuclease P Database - Brown - 1998
49	Recent improvements to the SMART domain-based sequence annotation resource - Letunic, Goodstadt, et al. - 2002
43	Recognition and parsing of context-free languages - Younger - 1967
34	Non-coding RNA genes and the modern RNA - Eddy - 2001
31	A polyhedral approach to RNA sequence structural alignment - Lanhof, Reinert, et al. - 1998
26	Kolodziejczak T: Inferring consensus structure from nucleic acid sequences - Chiu - 1991
25	RNAlign program: Alignment of RNA sequences using both primary and secondary structures - Corpet, Michot - 1994
21	Explaining and controlling ambiguity in dynamic programming - Giegerich - 2000
21	Mian IS, Haussler D: Dirichlet mixtures: a method for improving detection of weak but significant protein sequence homology. Comput Appl Biosci - Sjolander, Karplus, et al. - 1996
19	Identifying potential tRNA genes in genomic DNA sequences - Fichant, Burks - 1991
18	Overbeek R: Searching for patterns in genomic data. Trends Genet - Dsouza, Larsen - 1997
14	Zwieb C: SRP-RNA sequence alignment and secondary structure - Larsen - 1991
11	Haussler D: Stochastic context-free grammers for tRNA modeling. Nucleic Acids Research - Sakakibara, Brown, et al. - 1994
11	Waterman: Identification of common molecular subsequences - Smith, S - 1981
11	5s Ribosomal RNA database - Szymanski, Barciszewska, et al. - 2002
9	Very fast identification of RNA motifs in genomic DNA. Application to tRNA search in the yeast genome - El-Mabrouk, Lisacek - 1996
8	D and Gibson T: W Clustal: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res - Thompson, Higgins - 1994
6	F: Automatic identification of group I intron cores in genomic DNA sequences - Lisacek, Diaz, et al. - 1994
5	W and Lipman D Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res - Altschul, Madden, et al. - 1997
4	R Cedergren: An RNA pattern matching program with enhanced performance and portability - Laferriere, Gautheret - 1994
3	D Lipman: Improved Tools for Biological Sequence Comparison - Pearson - 1988
3	BC Orcutt: A model of evolutionary change in proteins - Dayhoff, Schwartz - 1978
3	SJ Young: Applications of stochastic context-free grammars using the inside-outside algorithm. Computer Speech and Language - Lari - 1991
3	Stormo G: Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res - Gutell, Power, et al. - 1992
3	A Misch, M Sprinzl: Compilation of tRNA sequences and sequences of tRNA genes - Steinberg - 1993
3	R De Wachter: Compilation of small ribosomal subunit RNA structures. Nucl. Acids Res - Neefs, Peer, et al. - 1993
2	A Hochberg, N de Groot, J Barciszewski: The non-coding RNAs as riboregulators - Erdmann, Barciszewska, et al.
2	MW Hentze: Finding the hairpin in the haystack: Searching for RNA motifs. Trends Genet - Dandekar - 1995
2	SR Eddy: tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl. Acids Res - Lowe - 1997
2	JP Bachellerie: Intron-encoded, antisense small nucleolar RNAs: The characterization of nine novel species points to their direct role as guides for the 2’-O-ribose methylation of rRNAs - Nicoloso, Qu, et al. - 1996
2	SR Eddy: A computational screen for methylation guide snoRNAs - Lowe - 1998
2	A Krogh, GJ Mitchison: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids - Durbin, Eddy - 1998
2	EA OBrien, DG Higgins: RAGA: RNA sequence alignment by genetic algorithm - Notredame
2	GD Stormo: Discovering common stem-loop motifs in unaligned RNA sequences - Gorodkin, Stricklin - 1994
2	DH Turner: Dynalign: an algorithm for finding the secondary structure common to two RNA sequences - Mathews
2	SJ Young: The estimation of stochastic context-free grammars using the inside-outside algorithm. Computer Speech and Language - Lari - 1990
2	R De Wachter: Database on the structure of large ribosomal subunit RNA. Nucl. Acids Res - Rijk, Peer, et al. - 1994
1	Computational genomics of noncoding RNA genes 2002 - Eddy