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Pairagon specifications


Unique identifier OMICS_13789
Name Pairagon
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes



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  • person_outline Michael Brent <>

Publication for Pairagon

Pairagon in publications

PMCID: 2766791
PMID: 20190955
DOI: 10.2174/138920209789177575

[…] based approach can achieve significant improvement over traditional progressive alignment algorithms []., pair-hmms have also been used for gene prediction [, -]. for example, a method called pairagon+n-scan_est provides a convenient pipeline for gene annotation by combining a pair-hmm with a de novo gene prediction algorithm []. in this method, a pair-hmm is first used to find accurate […]

PMCID: 1534067
PMID: 16817966
DOI: 10.1186/1471-2105-7-327

[…] the set of available full length cdnas. for example, we recently built a system in which the first stage is aligning full-orf cdna sequences to their native locus using our new cdna-genome aligner, pairagon []. the cds genbank annotations of the cdna sequences were used to convert these alignments into gene structures. where there is no full-length cdna to align, we used n-scan_est together […]

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Pairagon institution(s)
Department of Computer Science and Center for Genome Sciences, Washington University, St Louis, MO, USA; European Molecular Biology Laboratory, Heidelberg, Germany
Pairagon funding source(s)
This work was supported by the National Genome Research Institute under ENCODE Project (grant n°U54 HG004555) and the modENCODE Project (grant n°U01 HG004271).

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