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Locomotif specifications

Information


Unique identifier OMICS_08365
Name Locomotif
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Robert Giegerich

Publication for Locomotif

Locomotif citations

 (7)
library_books

RNA folding with hard and soft constraints

2016
PMCID: 4842303
PMID: 27110276
DOI: 10.1186/s13015-016-0070-z

[…] nto a specialized dynamic programming algorithm that computes the optimal folds or partition functions from the ensemble of structures that fit the prescribed scaffold. A convenient implementation is LocoMotif [], which is built on top of algebraic dynamic programming (ADP) []. Abstract shapes [] are a conceptually very similar way of specifying such scaffolds at different resolutions with the adv […]

call_split

Thermodynamic matchers for the construction of the cuckoo RNA family

2015
RNA Biol
PMCID: 4615179
PMID: 25779873
DOI: 10.1080/15476286.2015.1017206
call_split See protocol

[…] erleaf shape. This allows one to directly compute this shape's contribution to the partition function of x in O(n3), which otherwise requires computing all shapes and has exponential runtime.The tool Locomotif generates TDMs from structure graphics, which a non-programmer can compile from pre-defined building blocks (stems, bulges, multiloops, simple pseudoknots, …). These building blocks can be s […]

library_books

Two accurate sequence, structure, and phylogenetic template based RNA alignment systems

2013
BMC Syst Biol
PMCID: 3854672
PMID: 24565058
DOI: 10.1186/1752-0509-7-S4-S13

[…] in this family of programs, had a simple descriptor language that was easier to manually generate but was limited by the details in the structural constraints that can be identified. RNAMotif [] and Locomotif [] are newer programs that have a richer descriptor language with greater specificity and complexity of the RNA constraints that can be identified and distinguished. While these programs are […]

library_books

Bellman’s GAP—a language and compiler for dynamic programming in sequence analysis

2013
Bioinformatics
PMCID: 3582264
PMID: 23355290
DOI: 10.1093/bioinformatics/btt022

[…] r, are used in a Viterbi-like scoring algebra, akin to pfunc_id (cf. ). Inside scoring is simply achieved by replacing choice function max with sum, akin to pfunc.In ongoing work, we are adapting the Locomotif tool by to the MicroState grammar of to generate motif matchers coded in GAP-L from user-supplied structure graphics. Future users of Locomotif will be customers of Bellman’s GAP, possibly […]

library_books

Conservation and Occurrence of Trans Encoded sRNAs in the Rhizobiales

2011
Genes
PMCID: 3927594
PMID: 24710299
DOI: 10.3390/genes2040925

[…] a strongly conserved structure and low sequence similarity, except for a prominent loop motif (GAUGUA). shows a snapshot of TDM construction, where we depict a structure graphics with the help of the Locomotif editor [], annotate it with conserved sequence information and compiled it into a search program at the Bielefeld Bioinformatics Server [].TDMs tend to run a bit faster than CMs (when their […]

call_split

A genome wide survey of sRNAs in the symbiotic nitrogen fixing alpha proteobacterium Sinorhizobium meliloti

2010
BMC Genomics
PMCID: 2873474
PMID: 20398411
DOI: 10.1186/1471-2164-11-245
call_split See protocol

[…] fort in developing curated databases of aligned secondary structures, as a prerequisite for increasing the power of comparative analysis. Another perspective is that the use of structural models from Locomotif [], which include the thermodynamics of RNA folding and can handle simple cases of pseudoknots, may generalize better than the combinatorial pattern descriptions via RNAMotif [] used in the […]

Citations

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Locomotif institution(s)
Faculty of Technology, Bielefeld University, Bielefeld, Germany

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