Locomotif: from graphical motif description to RNA motif search

Reeder J, Reeder J, Giegerich R (2007)
In: Bioinformatics. Bioinformatics, 23(13). OXFORD UNIV PRESS: I392-I400.

Konferenzbeitrag | Veröffentlicht | Englisch
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Reeder, Janina; Reeder, Jens; Giegerich, RobertUniBi
Abstract / Bemerkung
Motivation and Results: Motivated by the recent rise of interest in small regulatory RNAs, we present Locomotif-a new approach for locating RNA motifs that goes beyond the previous ones in three ways: ( 1) motif search is based on efficient dynamic programming algorithms, incorporating the established thermodynamic model of RNA secondary structure formation. ( 2) motifs are described graphically, using a Java-based editor, and search algorithms are derived from the graphics in a fully automatic way. The editor allows us to draw secondary structures, annotated with size and sequence information. They closely resemble the established, but informal way in which RNA motifs are communicated in the literature. Thus, the learning effort for Locomotif users is minimal. ( 3) Locomotif employs a client-server approach. Motifs are designed by the user locally. Search programs are generated and compiled on a bioinformatics server. They are made available both for execution on the server, and for download as C source code plus an appropriate makefile.
Titel des Konferenzbandes
Serien- oder Zeitschriftentitel
Page URI


Reeder J, Reeder J, Giegerich R. Locomotif: from graphical motif description to RNA motif search. In: Bioinformatics. Bioinformatics. Vol 23. OXFORD UNIV PRESS; 2007: I392-I400.
Reeder, J., Reeder, J., & Giegerich, R. (2007). Locomotif: from graphical motif description to RNA motif search. Bioinformatics, Bioinformatics, 23, I392-I400. OXFORD UNIV PRESS. https://doi.org/10.1093/bioinformatics/btm179
Reeder, Janina, Reeder, Jens, and Giegerich, Robert. 2007. “Locomotif: from graphical motif description to RNA motif search”. In Bioinformatics, 23:I392-I400. Bioinformatics. OXFORD UNIV PRESS.
Reeder, J., Reeder, J., and Giegerich, R. (2007). “Locomotif: from graphical motif description to RNA motif search” in Bioinformatics Bioinformatics, vol. 23, (OXFORD UNIV PRESS), I392-I400.
Reeder, J., Reeder, J., & Giegerich, R., 2007. Locomotif: from graphical motif description to RNA motif search. In Bioinformatics. Bioinformatics. no.23 OXFORD UNIV PRESS, pp. I392-I400.
J. Reeder, J. Reeder, and R. Giegerich, “Locomotif: from graphical motif description to RNA motif search”, Bioinformatics, Bioinformatics, vol. 23, OXFORD UNIV PRESS, 2007, pp.I392-I400.
Reeder, J., Reeder, J., Giegerich, R.: Locomotif: from graphical motif description to RNA motif search. Bioinformatics. Bioinformatics. 23, p. I392-I400. OXFORD UNIV PRESS (2007).
Reeder, Janina, Reeder, Jens, and Giegerich, Robert. “Locomotif: from graphical motif description to RNA motif search”. Bioinformatics. OXFORD UNIV PRESS, 2007.Vol. 23. Bioinformatics. I392-I400.

19 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Characterization of mammalian Lipocalin UTRs in silico: Predictions for their role in post-transcriptional regulation.
Mejias A, Diez-Hermano S, Ganfornina MD, Gutierrez G, Sanchez D., PLoS One 14(3), 2019
PMID: 30840684
RNA folding with hard and soft constraints.
Lorenz R, Hofacker IL, Stadler PF., Algorithms Mol Biol 11(), 2016
PMID: 27110276
RNA motif search with data-driven element ordering.
Rampášek L, Jimenez RM, Lupták A, Vinař T, Brejová B., BMC Bioinformatics 17(1), 2016
PMID: 27188396
The RNA shapes studio.
Janssen S, Giegerich R., Bioinformatics 31(3), 2015
PMID: 25273103
Thermodynamic matchers for the construction of the cuckoo RNA family.
Reinkensmeier J, Giegerich R., RNA Biol 12(2), 2015
PMID: 25779873
Riboregulation in plant-associated α-proteobacteria.
Becker A, Overlöper A, Schlüter JP, Reinkensmeier J, Robledo M, Giegerich R, Narberhaus F, Evguenieva-Hackenberg E., RNA Biol 11(5), 2014
PMID: 25003187
Bellman's GAP--a language and compiler for dynamic programming in sequence analysis.
Sauthoff G, Möhl M, Janssen S, Giegerich R., Bioinformatics 29(5), 2013
PMID: 23355290
Alternative polyadenylation in glioblastoma multiforme and changes in predicted RNA binding protein profiles.
Shao J, Zhang J, Zhang Z, Jiang H, Lou X, Huang B, Foltz G, Lan Q, Huang Q, Lin B., OMICS 17(3), 2013
PMID: 23421905
Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems.
Shang L, Gardner DP, Xu W, Cannone JJ, Miranker DP, Ozer S, Gutell RR., BMC Syst Biol 7 Suppl 4(), 2013
PMID: 24565058
Feature-based 3D motif filtering for ribosomal RNA.
Shen Y, Wong HS, Zhang S, Yu Z., Bioinformatics 27(20), 2011
PMID: 21873638
Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales.
Reinkensmeier J, Schlüter JP, Giegerich R, Becker A., Genes (Basel) 2(4), 2011
PMID: 24710299
De novo prediction of structured RNAs from genomic sequences.
Gorodkin J, Hofacker IL, Torarinsson E, Yao Z, Havgaard JH, Ruzzo WL., Trends Biotechnol 28(1), 2010
PMID: 19942311
RNAsnoop: efficient target prediction for H/ACA snoRNAs.
Tafer H, Kehr S, Hertel J, Hofacker IL, Stadler PF., Bioinformatics 26(5), 2010
PMID: 20015949
Faster computation of exact RNA shape probabilities.
Janssen S, Giegerich R., Bioinformatics 26(5), 2010
PMID: 20080511
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti.
Schlüter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Jänicke S, Becker JD, Giegerich R, Becker A., BMC Genomics 11(), 2010
PMID: 20398411
Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA.
Majerfeld I, Chocholousova J, Malaiya V, Widmann J, McDonald D, Reeder J, Iyer M, Illangasekare M, Yarus M, Knight R., RNA 16(10), 2010
PMID: 20699302
Informatic resources for identifying and annotating structural RNA motifs.
George AD, Tenenbaum SA., Mol Biotechnol 41(2), 2009
PMID: 18979204
The tedious task of finding homologous noncoding RNA genes.
Menzel P, Gorodkin J, Stadler PF., RNA 15(12), 2009
PMID: 19861422
KnotInFrame: prediction of -1 ribosomal frameshift events.
Theis C, Reeder J, Giegerich R., Nucleic Acids Res 36(18), 2008
PMID: 18820303

26 References

Daten bereitgestellt von Europe PubMed Central.

Finding the genes in genomic DNA.
Burge CB, Karlin S., Curr. Opin. Struct. Biol. 8(3), 1998
PMID: 9666331
Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency.
Clote P, Ferre F, Kranakis E, Krizanc D., RNA 11(5), 2005
PMID: 15840812
Searching for patterns in genomic data.
Dsouza M, Larsen N, Overbeek R., Trends Genet. 13(12), 1997
PMID: 9433140
A discipline of dynamic programming over sequence data
Giegerich, Sci. Compu. Programm 51(), 2004
Abstract shapes of RNA.
Giegerich R, Voss B, Rehmsmeier M., Nucleic Acids Res. 32(16), 2004
PMID: 15371549
Rfam: annotating non-coding RNAs in complete genomes.
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A., Nucleic Acids Res. 33(Database issue), 2005
PMID: 15608160
Thermodynamic matchers: strengthening the significance of RNA folding energies
Höchsmann, 2006
Fast folding and comparison of RNA secondary structures
Hofacker, Monatsh. Chem 125(), 1994
Experimental approaches to identify non-coding RNAs.
Huttenhofer A, Vogel J., Nucleic Acids Res. 34(2), 2006
PMID: 16436800
An RNA pattern matching program with enhanced performance and portability.
Laferriere A, Gautheret D, Cedergren R., Comput. Appl. Biosci. 10(2), 1994
PMID: 7517334
RNAMotif, an RNA secondary structure definition and search algorithm.
Macke TJ, Ecker DJ, Gutell RR, Gautheret D, Case DA, Sampath R., Nucleic Acids Res. 29(22), 2001
PMID: 11713323
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
Mathews DH, Sabina J, Zuker M, Turner DH., J. Mol. Biol. 288(5), 1999
PMID: 10329189
Development of joint application strategies for two microbial gene finders.
McHardy AC, Goesmann A, Puhler A, Meyer F., Bioinformatics 20(10), 2004
PMID: 14988122

A graphical programming system for molecular motif search
Reeder, 2006
Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression.
Ruberg S, Tian ZX, Krol E, Linke B, Meyer F, Wang Y, Puhler A, Weidner S, Becker A., J. Biotechnol. 106(2-3), 2003
PMID: 14651866

Versatile and declarative dynamic programming using pair algebras.
Steffen P, Giegerich R., BMC Bioinformatics 6(), 2005
PMID: 16156887
Table design in dynamic programming
Steffen, Inf. Computa 204(), 2006
How to find small non-coding RNAs in bacteria.
Vogel J, Sharma CM., Biol. Chem. 386(12), 2005
PMID: 16336117
Fast and reliable prediction of noncoding RNAs.
Washietl S, Hofacker IL, Stadler PF., Proc. Natl. Acad. Sci. U.S.A. 102(7), 2005
PMID: 15665081

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

PMID: 17646322
PubMed | Europe PMC

Suchen in

Google Scholar