jpHMM statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

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


No version available

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 citations

 (83)
call_split

HIV 1 transmitted drug resistance in Slovenia and its impact on predicted treatment effectiveness: 2011–2016 update

2018
PLoS One
PMCID: 5919638
PMID: 29698470
DOI: 10.1371/journal.pone.0196670
call_split See protocol

[…] surveillance drug-resistance mutations (SDRMs) on the WHO list to unify TDR reporting between programs and countries [].The HIV-1 subtype was determined by using Rega version 3.0, Comet version 2.2, jpHMM-HIV, and SCUEAL [–].Fisher’s exact test was used for categorical data and t-statistics for continuous data using OpenEpi version 3.01; associations with p < 0.05 were considered significant []. […]

library_books

Early MinION™ nanopore single molecule sequencing technology enables the characterization of hepatitis B virus genetic complexity in clinical samples

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

[…] r sequence. As previously observed with clones, the deduced MinION consensus sequence showed >99% nucleotide identity compared to the Sanger sequence.The 472 nanopore sequences were analyzed with the jpHMM-HBV software (). Results identified four genotype D/E recombination breakpoints in the 213 sequences covering ≥ 95% of HBV genome. Similar results were obtained for nine additional sequences cov […]

library_books

Genotyping and sero virological characterization of hepatitis B virus (HBV) in blood donors, Southern Ethiopia

2018
PLoS One
PMCID: 5819820
PMID: 29462187
DOI: 10.1371/journal.pone.0193177

[…] tree was done by FigTree v.1.4.3 software. For independent cross-checking, a web-based NCBI genotyping tool []was used. Recombinant analysis was performed by online recombination detection method of jpHMM[]. The accession numbers of HBV isolates sequenced in this study have been deposited in GenBank asMF169791 to MF169875. […]

library_books

A high HIV 1 strain variability in London, UK, revealed by full genome analysis: Results from the ICONIC project

2018
PLoS One
PMCID: 5794160
PMID: 29389981
DOI: 10.1371/journal.pone.0192081

[…] D pair (accession numbers MF109354and MF109527, respectively). These two URF_50B sequences that formed a phylogenetic pair (genome-wide similarity = 96.2%) were classified as an A1/B/D recombinant by jpHMM, but after phylogenetic analysis of the recombinant segments, those assigned to A1 and D clustered with the recombinant CRF50_A1D (previously described in the UK []), and shared the same breakpo […]

call_split

The burden of hepatitis B virus (HBV) infection, genotypes and drug resistance mutations in human immunodeficiency virus positive patients in Northwest Ethiopia

2017
PLoS One
PMCID: 5744989
PMID: 29281718
DOI: 10.1371/journal.pone.0190149
call_split See protocol

[…] d pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach. All alignments and evolutionary analyses were conducted using MEGA7 []. HBV recombinant analysis was performed by jumping profile Hidden Markov Model (JpHMM) []. All sequences were submitted to GenBank (accession number pending). […]

library_books

Genomic characterization and molecular evolution analysis of subtype B and BF recombinant HIV 1 strains among Argentinean men who have sex with men reveal a complex scenario

2017
PLoS One
PMCID: 5731684
PMID: 29244833
DOI: 10.1371/journal.pone.0189705

[…] were selected considering both the type of analysis to be carried out and the nature of the database []. Initially, pol sequences were analyzed by three different methods or algorithms including: (i) Jumping profile Hidden Markov Model (jpHMM) method. It is based on a pre-calculated multiple alignment of the major HIV-1 subtypes where each one is represented by a profile hidden Markov model furthe […]

Citations

Looking to check out a full list of citations?

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

jpHMM reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review jpHMM