OMA protocols

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OMA specifications

Information


Unique identifier OMICS_24727
Name OMA
Alternative name Optimal Multiple Alignment
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Source code URL https://bibiserv.cebitec.uni-bielefeld.de/applications/oma/resources/downloads/oma-0.98-src.tar.gz
Maintained Yes

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Maintainer


  • person_outline Jens Stoye <>

Publication for Optimal Multiple Alignment

OMA in pipelines

 (2)
2011
PMCID: 3296468
PMID: 22094861
DOI: 10.1093/gbe/evr120

[…] ) and the ensembl (version 55; ) databases. sequences that showed significant homology to the queries were retrieved from the databases. after partial and redundant sequences had been removed, an optimal multiple alignment of their amino acid sequences was constructed using the xced alignment editor implementing the mafft program (). using regions in which alignment was unambiguous […]

2005
PMCID: 1242226
PMID: 16150145
DOI: 10.1186/1471-2164-6-114

[…] a signal peptide prediction program, 14 of the 53 freps were predicted to contain secretion signal peptides (table ), suggesting that freps can be extracellular or intracellular., to construct an optimal multiple alignment of the fbg domain, we first aligned selected sequences with the t_coffee program; this was followed by refinements on the basis of the psi-blast search results. […]


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OMA in publications

 (12)
PMCID: 4959381
PMID: 27455061
DOI: 10.1186/s12859-016-1128-0

[…] the iterative computation of theses matrices is started with the initial values: ha(i,0)=ha(0,j)=e(i,0)=f(0,j)=0 for all 0<=i<=q, 0<=j<=s., the time complexity of computing an optimal multiple alignment of more than two sequences grows exponentially in terms of the number of input sequences. thus, heuristic approaches with polynomial complexities must be used in practice […]

PMCID: 4122933
PMID: 24951566
DOI: 10.1093/gbe/evu135

[…] in situ hybridizations on paraffin-embedded sections for adult eyes of zebrafish, xenopus, and green anole were performed using the aforementioned riboprobes as previously described ()., an optimal multiple alignment of all retrieved cdna sequences was constructed using mega5 (), in which the muscle program () is implemented. molecular phylogenetic trees were inferred using regions […]

PMCID: 3762194
PMID: 23843192
DOI: 10.1093/gbe/evt104

[…] enc homologs were retrieved from the ensembl genome database and national center for biotechnology information (ncbi) protein database, by performing blastp searches () using human enc1 as query. an optimal multiple alignment of the retrieved enc amino acid sequences including the query sequence was constructed (b) using the alignment editor xced in which the mafft program is implemented (). […]

PMCID: 3694645
PMID: 23813006
DOI: 10.1093/bioinformatics/btt215

[…] to alleviate this problem, we have created a multiple alignment of the 1092 individuals manually by integrating only known snps from each individual, respectively, into chromosome 18 of grch37; the optimal multiple alignment is trivial for this scenario. we have also created a reference multi-genome with snps only from the 1092 individuals for bwbble. the gcsa index construction took 1.87 h, […]

PMCID: 3546004
PMID: 22920415
DOI: 10.1186/1471-2105-13-214

[…] in the selected reference may artificially decrease the quality and score of the alignment. hence, we can not guarantee that the multiple alignment will be within a specific error bound of the optimal multiple alignment. nontheless, our method performs well in practice, which will be discussed in detail in the results section., we finally obtain a dense matrix of aligned feature vector […]


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OMA institution(s)
Celera Genomics, Informatics Research, Rockville, MD, USA; German Cancer Research Center (DKFZ), Theoretical Bioinformatics (H0300), Heidelberg, Germany; Universitat Bielefeld, Research Center for Interdisciplinary Studies on Structure Formation (FSPM), Bielefeld, Germany

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