jMHC statistics

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Associated diseases

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jMHC specifications

Information


Unique identifier OMICS_00300
Name jMHC
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Database management system SQLite
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.5.1706
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Michal Stuglik <>

Publication for jMHC

jMHC in publications

 (7)
PMCID: 5534077
PMID: 28754172
DOI: 10.1186/s13104-017-2654-1

[…] q30 []. finally, sequences were demultiplexed, trimmed of their tags and primer sequences, then summarised in a table listing the read number (read depth) of each sequence in each amplicon using jmhc []. in the case of the 454 data, the raw fasta file was processed by jmhc in the same manner., only variants between 239 and 242 bp in length (classical mhc class i genes) were retained […]

PMCID: 5497381
PMID: 28679358
DOI: 10.1186/s12862-017-0997-9

[…] 454 flx run according to the 454 amplicon sequencing protocols provided by the manufacturer (roche 454) at the functional genomics center, uni ⁄eth zurich. the sequencing output was analysed using jmhc software []. the jmhc software extracts reads according to primer sequence and tags that indicate individual identity and generates a table of variants (alleles) present in each individual along […]

PMCID: 4875725
PMID: 27206579
DOI: 10.1186/s12862-016-0681-5

[…] instructions. purified products were pooled in equimolar concentrations and sequenced commercially (macrogen, korea) on an eighth plate on a 454 gs-flx run., following 454 sequencing, we used the jmhc software [] to extract sequences and assign reads to individuals. only reads showing a complete match to the forward and reverse primers were retained, ensuring that all assigned reads covered […]

PMCID: 4306961
PMID: 25623996
DOI: 10.1038/srep08056

[…] run., reads containing the complete target primers and barcodes were extracted from the multifasta output file and de-multiplexed on the basis of the barcode and loci specific primer sequences using jmhc. the different sequences were compared to the known haplotype or genotype to determine correct sequences in geneious v6.1.7 (biomatters, auckland, nz). these previously known sequences […]

PMCID: 4369332
PMID: 25802816
DOI: 10.7717/peerj.853

[…] national museum of nature and science in tsukuba, japan., amplicons were bi-directionally sequenced, and reads that passed the initial 454 roche junior quality filter were de-multiplexed using jmhc (). jmhc is especially efficient for de-multiplexing bi-directionally sequenced double-tagged amplicons because it bins only those sequences that contain both forward and reverse primers […]


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jMHC institution(s)
Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
jMHC funding source(s)
Supported by the Foundation for Polish Science, professor subsidy 9⁄2008 and the Jagiellonian University (DS⁄WBINOZ⁄INOS⁄762⁄10).

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