RScan: Fast searching structural similarities for structured RNAs in large databases

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Xue, Chenghai ^a   Liu, Guo Ping ^b,c  

^a TSINGHUA UNIVERSITY   (China)

^b UNIVERSITY OF GLAMORGAN   (United Kingdom)

^c INSTITUTE OF AUTOMATION   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RIBOSOME RNA; RNA; RNA PRECURSOR; TRANSFER RNA;

ALGORITHM; ARTICLE; CHROMOSOME 21; COMPUTER ANALYSIS; COMPUTER PROGRAM; DATA BASE; GENOME ANALYSIS; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; NONHUMAN; NUCLEOTIDE SEQUENCE; RNA STRUCTURE; SEARCH ENGINE; STRUCTURAL HOMOLOGY; ANIMAL; CHEMISTRY; CHROMOSOME MAP; COMPARATIVE STUDY; CONFORMATION; EVALUATION; HUMAN; HUMAN CHROMOSOME; INFORMATION PROCESSING; METHODOLOGY; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ALGORITHMS; ANIMALS; AUTOMATIC DATA PROCESSING; BASE SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN; DATABASES, NUCLEIC ACID; HUMANS; MICRORNAS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 34547995219     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-257     Document Type: Article

References (30)

1. Klein RJ Eddy SR RSEARCH: Finding homologs of single structured RNA sequences BMC Bioinformatics 2003 4 1 44 239859 14499004 10.1186/ 1471-2105-4-44
2. Eddy SR Non-coding RNA genes and the modern RNA world Nat Rev Genet 2001 2 12 919-929 10.1038/35103511 11733745
3. Eddy SR Computational genomics of noncoding RNA genes Cell 2002 109 2 137-140 10.1016/S0092-8674(02)00727-4 12007398
4. Rivas E Eddy SR Noncoding RNA gene detection using comparative sequence analysis BMC Bioinformatics 2001 2 1 8 64605 11801179 10.1186/ 1471-2105-2-8
5. di Bernardo D Down T Hubbard T ddbRNA: Detection of conserved secondary structures in multiple alignments Bioinformatics 2003 19 13 1606-1611 10.1093/bioinformatics/btg229 12967955
6. Coventry A Kleitman DJ Berger B MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure Proc Natl Acad Sci U S A 2004 101 33 12102-12107 514400 15304649 10.1073/pnas.0404193101
7. Washietl S Hofacker IL Stadler PF Fast and reliable prediction of noncoding RNAs Proc Natl Acad Sci U S A 2005 102 7 2454-2459 548974 15665081 10.1073/pnas.0409169102
8. Washietl S Hofacker IL Lukasser M Huttenhofer A Stadler PF Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome Nat Biotechnol 2005 23 11 1383-1390 10.1038/nbt1144 16273071
9. Macke TJ Ecker DJ Gutell RR Gautheret D Case DA Sampath R RNAMotif, an RNA secondary structure definition and search algorithm Nucleic Acids Res 2001 29 22 4724-4735 92549 11713323 10.1093/nar/29.22.4724
10. Gautheret D Lambert A Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles J Mol Biol 2001 313 5 1003-1011 10.1006/jmbi.2001.5102 11700055
11. Hoechsmann M Toeller T Giegerich R Kurtz S Local Similarity in RNA Secondary Structures Proc Computational Systems Bioinformatics Conf 2003 2 159-168
12. Hofacker IL Vienna RNA secondary structure server Nucleic Acids Res 2003 31 13 3429-3431 169005 12824340 10.1093/nar/gkg599
13. Hofacker IL Priwitzer B Stadler PF Prediction of locally stable RNA secondary structures for genome-wide surveys Bioinformatics 2004 20 2 186-190 10.1093/bioinformatics/btg388 14734309
14. Havgaard JH Lyngso RB Stormo GD Gorodkin J Pairwise local structural alignment of RNA sequences with sequence similarity less than 40% Bioinformatics 2005 21 9 1815-1824 10.1093/bioinformatics/bti279 15657094
15. Pavesi G Mauri G Stefani M Pesole G RNAProfile: An algorithm for finding conserved secondary structure motifs in unaligned RNA sequences Nucleic Acids Res 2004 32 10 3258-3269 434454 15199174 10.1093/nar/gkh650
16. Liu J Wang JT Hu J Tian B A method for aligning RNA secondary structures and its application to RNA motif detection BMC Bioinformatics 2005 6 1 89 1090556 15817128 10.1186/1471-2105-6-89
17. Freyhult EK Bollback JP Gardner PP Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA Genome Res 2007 17 1 117-125 1716261 17151342 10.1101/ gr.5890907
18. Bafna V Zhang S FastR: Fast database search tool for non-coding RNA 2004 52-61 16447999
19. Weinberg Z Ruzzo WL Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy Bioinformatics 2004 20 Suppl 1 I334-I341 15262817 10.1093/bioinformatics/bth925
20. Weinberg Z Ruzzo WL Faster genome annotation of non-coding RNA families without loss of accuracy ACM Press 243-251
21. Ning Z Cox AJ Mullikin JC SSAHA: A fast search method for large DNA databases Genome Res 2001 11 10 1725-1729 311141 11591649 10.1101/ gr.194201
22. Smith TF Waterman MS Identification of common molecular subsequences J Mol Biol 1981 147 1 195-197 10.1016/0022-2836(81)90087-5 7265238
23. Hofacker IL Fontana W Stadler PF Bonhoeffer S Tacker M Schuster P Fast folding and comparison of RNA secondary structures Monatshefte f Chemie 1994 125 167-188 10.1007/BF00818163
24. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990 215 3 403-410 2231712
25. Griffiths-Jones S Bateman A Marshall M Khanna A Eddy SR Rfam: An RNA family database Nucleic Acids Res 2003 31 1 439-441 165453 12520045 10.1093/nar/gkg006
26. Bafna V Zhang S FastR: Fast database search tool for non-coding RNA Proc IEEE Comput Syst Bioinform Conf 2004 52-61 16447999
27. Sankoff D Simultaneous solution of the RNA folding, alignment and protosequence problems SIAM J Appl Math 1985 45 810-825 10.1137/0145048
28. Bonnet E Wuyts J Rouze P Van de Peer Y Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences Bioinformatics 2004 20 17 2911-2917 10.1093/bioinformatics/bth374 15217813
29. Griffiths-Jones S Moxon S Marshall M Khanna A Eddy SR Bateman A Rfam: annotating non-coding RNAs in complete genomes Nucleic Acids Res 2005 33 Database issue D121-4 540035 15608160 10.1093/nar/gki081
30. Griffiths-Jones S The microRNA Registry Nucleic Acids Res 2004 32 Database issue D109 11 10.1093/nar/gkh023