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Citations per year

Number of citations per year for the bioinformatics software tool OSfinder

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This map represents all the scientific publications referring to OSfinder per scientific context
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OSfinder specifications


Unique identifier OMICS_11715
Name OSfinder
Alternative name Orthologous Segment finder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Genomic locations of anchors
Output data Genomic locations of chains and orthologous segments
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.4
Stability Stable
Maintained Yes


No version available

Publication for Orthologous Segment finder

OSfinder citations


Pan genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite

BMC Genomics
PMCID: 4405911
PMID: 25898829
DOI: 10.1186/s12864-015-1488-2

[…] We used a two-step based approach for the identification of orthologous proteins across all 18 Pseudomonas genomes. First step i.e. whole genome based multiple alignments using Murasaki [] and OSfinder v1.4 [], revealed protein families including but not limited to; two-component system, DNA replication associated proteins, ribosomal subunit forming proteins, recombinase, bacterioferritins, […]


Reconstructing an ancestral genotype of two hexachlorocyclohexane degrading Sphingobium species using metagenomic sequence data

PMCID: 3906814
PMID: 24030592
DOI: 10.1038/ismej.2013.153

[…] omologous anchors were computed in two subspecies using Murasaki () with seed weight-30 and seed length-40. Pre-computed homologous anchors were treated as input to predict orthologous segments using OSfinder algorithm (). OSfinder predicts orthologous segments (syntenic) using Markov chain models and machine learning techniques. The advantage of using OSfinder lies in its automatic optimization o […]


Detecting long tandem duplications in genomic sequences

BMC Bioinformatics
PMCID: 3464658
PMID: 22568762
DOI: 10.1186/1471-2105-13-83

[…] enome self-alignment software. These anchors are then chained into larger (duplicated) segments, similarly to what is done in synteny or segmental duplication detection tools such as DAGchainer [] or OSfinder [], modified to account for the specific properties of tandem duplications. In the next step, we analyse these chains to find tandem regions and an associated duplication unit. This duplicati […]


Efficient large scale protein sequence comparison and gene matching to identify orthologs and co orthologs

Nucleic Acids Res
PMCID: 3315314
PMID: 22210858
DOI: 10.1093/nar/gkr1261

[…] relationships. Several computational algorithms have been developed to match genes between a pair of genomes in an effort to identify orthologs including MAGIC (), FISH (), DAGchainer (), ADHoRe (), OSfinder () and EGM (). As more and more complex genomes are being sequenced, especially eukaryotics genomes, identifying relationships between genes has become more complex. Identifying one-to-one or […]

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OSfinder institution(s)
Department of Biosciences and Informatics, Keio University, Japan; Department of Computer and Informatics Science, Seikei University, Japan
OSfinder funding source(s)
Ministry of Education, Culture, Sports, Science and Technology of Japan Grant-in-Aid for Scientific Research on Priority Area ‘Comparative Genomics’ (No. 17018029)

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