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OSfinder specifications

Information


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

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Publication for Orthologous Segment finder

OSfinder in publications

 (4)
PMCID: 4405911
PMID: 25898829
DOI: 10.1186/s12864-015-1488-2

[…] of 400 genes based phylogenetic tree. these 18 pseudomonas strains were then used for further comprehensive comparative genomic analysis., orthologous segments were determined using murasaki [] and osfinder v1.4 (orthologous-segment finder) [] for all 18 pseudomonas genomes. short homologous regions called anchors were determined between the genomes using murasaki at 28 and 36, weight […]

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

[…] 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 […]

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

[…] 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. […]

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 […]


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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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