TY - JOUR AU - Mattick, J. S. AU - Makunin, I. V. PY - 2006 DA - 2006// TI - Non-coding RNA JO - Hum Mol Genet VL - 15 UR - https://doi.org/10.1093/hmg/ddl046 DO - 10.1093/hmg/ddl046 ID - Mattick2006 ER - TY - JOUR AU - Mehler, M. F. AU - Mattick, J. S. PY - 2006 DA - 2006// TI - Non-coding RNAs in the nervous system JO - J Physiol VL - 575 UR - https://doi.org/10.1113/jphysiol.2006.113191 DO - 10.1113/jphysiol.2006.113191 ID - Mehler2006 ER - TY - JOUR AU - Eddy, S. R. PY - 1998 DA - 1998// TI - Profile hidden Markov models JO - Bioinformatics VL - 14 UR - https://doi.org/10.1093/bioinformatics/14.9.755 DO - 10.1093/bioinformatics/14.9.755 ID - Eddy1998 ER - TY - JOUR AU - Nawrocki, E. P. AU - Eddy, S. R. PY - 2007 DA - 2007// TI - Query-Dependent Banding (QDB) for faster RNA similarity searches JO - PLoS Computational Biology VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030056 DO - 10.1371/journal.pcbi.0030056 ID - Nawrocki2007 ER - TY - JOUR AU - Gardner, P. P. AU - Wilm, A. AU - Washietl, S. PY - 2005 DA - 2005// TI - A benchmark of multiple sequence alignment programs based upon structural RNAs JO - Nucleic Acids Research VL - 33 UR - https://doi.org/10.1093/nar/gki541 DO - 10.1093/nar/gki541 ID - Gardner2005 ER - TY - JOUR AU - Smith, T. F. AU - Waterman, M. S. PY - 1981 DA - 1981// TI - Identification of common molecular subsequences JO - J Mol Biol VL - 147 UR - https://doi.org/10.1016/0022-2836(81)90087-5 DO - 10.1016/0022-2836(81)90087-5 ID - Smith1981 ER - TY - JOUR AU - Freyhult, E. K. AU - Bollback, J. P. AU - Gardner, P. P. PY - 2007 DA - 2007// TI - Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.5890907 DO - 10.1101/gr.5890907 ID - Freyhult2007 ER - TY - JOUR AU - Iyer, S. AU - Deutsch, K. AU - Yan, X. AU - Lin, B. PY - 2007 DA - 2007// TI - Batch RNAi selector: a standalone program to predict specific siRNA candidates in batches with enhanced sensitivity JO - Comput Methods Programs Biomed VL - 85 UR - https://doi.org/10.1016/j.cmpb.2006.11.004 DO - 10.1016/j.cmpb.2006.11.004 ID - Iyer2007 ER - TY - JOUR AU - Klein, R. J. AU - Eddy, S. R. PY - 2003 DA - 2003// TI - RSEARCH: finding homologs of single structured RNA sequences JO - BMC Bioinformatics VL - 4 UR - https://doi.org/10.1186/1471-2105-4-44 DO - 10.1186/1471-2105-4-44 ID - Klein2003 ER - TY - JOUR AU - Numata, K. AU - Kanai, A. AU - Saito, R. AU - Kondo, S. AU - Adachi, J. AU - Wilming, L. G. AU - Hume, D. A. AU - Hayashizaki, Y. AU - Tomita, M. PY - 2003 DA - 2003// TI - Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1011603 DO - 10.1101/gr.1011603 ID - Numata2003 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - JOUR AU - Miyazawa, S. PY - 1995 DA - 1995// TI - A reliable sequence alignment method based upon probabilities residue correspondences JO - Protein Engineering VL - 8 UR - https://doi.org/10.1093/protein/8.10.999 DO - 10.1093/protein/8.10.999 ID - Miyazawa1995 ER - TY - JOUR AU - Muckstein, U. AU - Hofacker, I. L. AU - Stadler, P. F. PY - 2002 DA - 2002// TI - Stochastic pairwise alignments JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.suppl_2.S153 DO - 10.1093/bioinformatics/18.suppl_2.S153 ID - Muckstein2002 ER - TY - JOUR AU - Roshan, U. AU - Livesay, D. R. PY - 2006 DA - 2006// TI - Probalign: multiple sequence alignment using partition function posterior probabilities JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl472 DO - 10.1093/bioinformatics/btl472 ID - Roshan2006 ER - TY - JOUR AU - Do, C. B. AU - Mahabhashyam, M. S. AU - Brudno, M. AU - Batzoglou, S. PY - 2005 DA - 2005// TI - ProbCons: Probabilistic consistency-based multiple sequence alignment JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.2821705 DO - 10.1101/gr.2821705 ID - Do2005 ER - TY - JOUR AU - Katoh, K. AU - Misawa, K. AU - Kuma, K. AU - Miyata, T. PY - 2002 DA - 2002// TI - MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/gkf436 DO - 10.1093/nar/gkf436 ID - Katoh2002 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: a multiple sequence alignment method with reduced time and space complexity JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-113 DO - 10.1186/1471-2105-5-113 ID - Edgar2004 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - JOUR AU - Thompson, J. D. AU - Koehl, P. AU - Ripp, R. AU - Poch, O. PY - 2005 DA - 2005// TI - BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark JO - Proteins VL - 61 UR - https://doi.org/10.1002/prot.20527 DO - 10.1002/prot.20527 ID - Thompson2005 ER - TY - JOUR AU - Mizuguchi, K. AU - Deane, C. M. AU - Blundell, T. L. AU - Overington, J. P. PY - 1998 DA - 1998// TI - HOMSTRAD: a database of protein structure alignments for homologous families JO - Protein Sci VL - 7 UR - https://doi.org/10.1002/pro.5560071126 DO - 10.1002/pro.5560071126 ID - Mizuguchi1998 ER - TY - JOUR AU - Raghava, G. P. AU - Searle, S. M. AU - Audley, P. C. AU - Barber, J. D. AU - Barton, G. J. PY - 2003 DA - 2003// TI - OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy JO - BMC Bioinformatics VL - 4 UR - https://doi.org/10.1186/1471-2105-4-47 DO - 10.1186/1471-2105-4-47 ID - Raghava2003 ER - TY - JOUR AU - Thompson, J. D. AU - Higgins, D. G. AU - Gibson, T. J. PY - 1994 DA - 1994// TI - CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.22.4673 DO - 10.1093/nar/22.22.4673 ID - Thompson1994 ER - TY - JOUR AU - Cochrane, G. AU - Aldebert, P. AU - Althorpe, N. AU - Andersson, M. AU - Baker, W. AU - Baldwin, A. AU - Bates, K. AU - Bhattacharyya, S. AU - Browne, P. AU - van den Broek, A. PY - 2006 DA - 2006// TI - EMBL Nucleotide Sequence Database: developments in 2005 JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj130 DO - 10.1093/nar/gkj130 ID - Cochrane2006 ER - TY - JOUR AU - Griffiths-Jones, S. AU - Moxon, S. AU - Marshall, M. AU - Khanna, A. AU - Eddy, S. R. AU - Bateman, A. PY - 2005 DA - 2005// TI - Rfam: annotating non-coding RNAs in complete genomes JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki081 DO - 10.1093/nar/gki081 ID - Griffiths-Jones2005 ER - TY - STD TI - Personal communication with Alex Bateman of the RFAM database team ID - ref25 ER - TY - JOUR AU - Rivas, E. AU - Eddy, S. R. PY - 2001 DA - 2001// TI - Noncoding RNA gene detection using comparative sequence analysis JO - BMC Bioinformatics VL - 2 UR - https://doi.org/10.1186/1471-2105-2-8 DO - 10.1186/1471-2105-2-8 ID - Rivas2001 ER - TY - JOUR AU - Washietl, S. AU - Hofacker, I. L. AU - Stadler, P. F. PY - 2005 DA - 2005// TI - Fast and reliable prediction of noncoding RNAs JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0409169102 DO - 10.1073/pnas.0409169102 ID - Washietl2005 ER - TY - JOUR AU - Coventry, A. AU - Kleitman, D. J. AU - Berger, B. PY - 2004 DA - 2004// TI - Multiple sequence alignments for statistical detection of RNA secondary structure JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0404193101 DO - 10.1073/pnas.0404193101 ID - Coventry2004 ER - TY - JOUR AU - Phuong, T. M. AU - Do, C. B. AU - Edgar, R. C. AU - Batzoglou, S. PY - 2006 DA - 2006// TI - Multiple alignment of protein sequences with repeats and rearrangements JO - Nucleic Acids Research VL - 34 UR - https://doi.org/10.1093/nar/gkl511 DO - 10.1093/nar/gkl511 ID - Phuong2006 ER - TY - JOUR AU - Grice, J. A. AU - Hughey, R. AU - Speck, D. PY - 1997 DA - 1997// TI - Reduced space sequence alignment JO - CABIOS VL - 13 ID - Grice1997 ER - TY - STD TI - RNA-genome alignment benchmark and tools website[http://www.cs.njit.edu/usman/RNAgenome] UR - http://www.cs.njit.edu/usman/RNAgenome ID - ref31 ER - TY - BOOK AU - Mount, D. W. PY - 2006 DA - 2006// TI - Bioinformatics: sequence and genome analysis PB - Cold Spring Harbor Laboratory Press CY - Cold Spring Harbor, NY ID - Mount2006 ER - TY - JOUR AU - Pearson, W. R. PY - 1995 DA - 1995// TI - Comparison of methods for searching protein sequence databases JO - Protein Science VL - 4 UR - https://doi.org/10.1002/pro.5560040613 DO - 10.1002/pro.5560040613 ID - Pearson1995 ER - TY - JOUR AU - Hulsen, T. AU - de Vlieg, J. A. M. AU - Leunissen, J. M. A. AU - Groenen, P. PY - 2006 DA - 2006// TI - Testing statistical significance scores of sequence comparison methods with structure similarity JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-444 DO - 10.1186/1471-2105-7-444 ID - Hulsen2006 ER - TY - BOOK AU - Kanji, G. K. PY - 2006 DA - 2006// TI - 100 Statistical tests ID - Kanji2006 ER - TY - JOUR AU - Thompson, J. D. AU - Plewniak, F. AU - Poch, O. PY - 1999 DA - 1999// TI - BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs JO - Bioinformatics VL - 15 UR - https://doi.org/10.1093/bioinformatics/15.1.87 DO - 10.1093/bioinformatics/15.1.87 ID - Thompson1999 ER - TY - JOUR AU - Gribskov, M. AU - Robinson, N. L. PY - 1996 DA - 1996// TI - Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching JO - Comput Chem VL - 20 UR - https://doi.org/10.1016/S0097-8485(96)80004-0 DO - 10.1016/S0097-8485(96)80004-0 ID - Gribskov1996 ER -