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OMA specifications


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
Maintained Yes


No version available


  • person_outline Jens Stoye

Publication for Optimal Multiple Alignment

OMA citations


Parallel algorithms for large scale biological sequence alignment on Xeon Phi based clusters

BMC Bioinformatics
PMCID: 4959381
PMID: 27455061
DOI: 10.1186/s12859-016-1128-0

[…] 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 fo […]


RNA motif discovery: a computational overview

Biol Direct
PMCID: 4600295
PMID: 26453353
DOI: 10.1186/s13062-015-0090-5

[…] sequences based on comparative sequence analysis.Each iteration in the algorithm involves two steps: (i) Given the current alignment, build an optimal CM and (ii) given the current CM model, find the optimal multiple alignment between the sequences. Essentially, the algorithm is trying to learn the structure and the associated parameters simultaneously. The first step is achieved by a DP algorithm […]


Evolution of the Vertebrate Pax4/6 Class of Genes with Focus on Its Novel Member, the Pax10 Gene

Genome Biol Evol
PMCID: 4122933
PMID: 24951566
DOI: 10.1093/gbe/evu135

[…] 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 of se […]


Saltatory Evolution of the Ectodermal Neural Cortex Gene Family at the Vertebrate Origin

Genome Biol Evol
PMCID: 3762194
PMID: 23843192
DOI: 10.1093/gbe/evt104
call_split See protocol

[…] 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 (). Simi […]


Short read alignment with populations of genomes

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, whe […]


Combining peak and chromatogram based retention time alignment algorithms for multiple chromatography mass spectrometry datasets

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

[…] absent 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 indice […]

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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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