jpHMM pipeline

jpHMM specifications

Information


Unique identifier OMICS_06323
Name jpHMM
Alternative name jumping profile Hidden Markov Model
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Viruses
    • Hepatitis B virus
    • Human immunodeficiency virus 1
    • Human immunodeficiency virus 2

Versioning


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Maintainer


  • person_outline jpHMM Team <>

Information


Unique identifier OMICS_06323
Name jpHMM
Alternative name jumping profile Hidden Markov Model
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Viruses
    • Hepatitis B virus
    • Human immunodeficiency virus 1
    • Human immunodeficiency virus 2

Maintainer


  • person_outline jpHMM Team <>

Publication for jumping profile Hidden Markov Model

jpHMM IN pipelines

 (8)
2018
PMCID: 5864009
PMID: 29566006
DOI: 10.1371/journal.pone.0194366

[…] loman et al. [16]. a single round of correction was carried out for each individual sample., breakpoint positions for genomic recombination in hbv whole genome sequences were determined by using the jumping profile hidden markov model (jphmm-hbv) available at the department of bioinformatics of the göttingen university, germany (http://jphmm.gobics.de/submission_hbv) [17]. sequence position […]

2018
PMCID: 5864009
PMID: 29566006
DOI: 10.1371/journal.pone.0194366

[…] correction was carried out for each individual sample., breakpoint positions for genomic recombination in hbv whole genome sequences were determined by using the jumping profile hidden markov model (jphmm-hbv) available at the department of bioinformatics of the göttingen university, germany (http://jphmm.gobics.de/submission_hbv) [17]. sequence position numbers are provided according to an hbv […]

2018
PMCID: 5864009
PMID: 29566006
DOI: 10.1371/journal.pone.0194366

[…] in hbv whole genome sequences were determined by using the jumping profile hidden markov model (jphmm-hbv) available at the department of bioinformatics of the göttingen university, germany (http://jphmm.gobics.de/submission_hbv) [17]. sequence position numbers are provided according to an hbv genotype a reference sequence (genbank am282986)., integrative genomics viewer (igv) browser (version […]

2017
PMCID: 5536263
PMID: 28759645
DOI: 10.1371/journal.pone.0182376

[…] main circulating recombinant forms (crfs) were used to identify and designate hiv-1 subtypes (s1 table). recombinant subtype analysis was performed using a combination of hiv-1 genotyping tool[10], jumping profile hidden markov model [11], visual inspection, and construction of subregion ml trees with bootstrap analyses to confirm breakpoint assignments. bootstrap values of 95 percent or higher […]

2014
PMCID: 4214716
PMID: 25356726
DOI: 10.1371/journal.pone.0110738

[…] c, crf07_bc related sequences. if there was evidence of recombination in any of the sequences (i.e., discordant gene regions or outlier position in a tree), they were further analyzed using the jumping profile hidden markov model program (jphmm; http://jphmm.gobics.de/) [19]. in order to confirm the possible recombinant structures and identify recombinant breakpoints of the potential hiv-1 […]

jpHMM institution(s)
Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany

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