microHarvester protocols

View microHarvester computational protocol

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microHarvester specifications

Information


Unique identifier OMICS_22738
Name microHarvester
Interface Web user interface
Restrictions to use None
Input data A miRNA precursor sequence plus mature miRNA sequence.
Output data An overview document generated for each miRNA query.
Output format PDF
Computer skills Basic
Maintained Yes

Maintainer


  • person_outline Tobias Dezulian <>

Additional information


microHARVESTER is offered as a web-service and additionally as source code upon request

Publication for microHarvester

microHarvester in pipeline

2007
PMCID: 1838911
PMID: 17359535
DOI: 10.1186/1471-2229-7-13

[…] of mirna sequences is a feature which can be used to find mirnas which are homologous to an already identified mirna from another plant species. such a strategy is implemented in the tool microharvester [] which we used to identify homologs to known mirnas (mirbase) in genomic trace files and est sequences allowing a maximum number of eight unpaired nucleotides within the mature mirna […]


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microHarvester in publications

 (7)
PMCID: 5015389
PMID: 27385424
DOI: 10.1161/JAHA.116.003521

[…] was added to the medium with or without 100 μmol/l pe for a further 48 hours. after washing (2 times) with pbs, the cells were harvested using trypsin and attached to glass filter mats using a microharvester, and radioactivity was measured using a liquid scintillation counter (wallac β‐plate, turku, finland)., total rna was extracted from the samples using trizol reagent (invitrogen). cdna […]

PMCID: 4493087
PMID: 26148191
DOI: 10.1371/journal.pone.0131579

[…] 18 h, 0.5 μci [3h]-thymidine (perkin-elmer, waltham, ma) was added to each well. after 8 h, the media was removed and the cells were dissociated in 10x trypsin-edta and harvested using a 12-channel microharvester (skatron instruments, norway). the samples were counted in a liquid scintillation spectrophotometer. all conditions were in quadruplicate, and each experiment repeated at least twice., […]

PMCID: 3565333
PMID: 23344055
DOI: 10.3390/ijms14011516

[…] revealed the existence of a diverse mirna repertoire including highly conserved mirna families [,,,,]. conserved mirnas families between p. patens and other land plants were discovered using the microharvester algorithm that analyszes and predicts conserved mir genes in genomic sequences []. the reported p. patens mirnas were identified from wild type plants covering major developmental […]

PMCID: 2822795
PMID: 19939267
DOI: 10.1186/1471-2164-10-558

[…] analyses were performed on berries - organs of particular agronomic importance - from other clones as they cannot be easily obtained from the very weak pn40024 clone., we previously used the microharvester software [] with all plant mirnas present in release 9.1 of mirbase [] to identify 164 candidate conserved mirnas and their precursors in the 8.4 fold coverage assembly of the genome […]

PMCID: 1838911
PMID: 17359535
DOI: 10.1186/1471-2229-7-13

[…] specific precursor was identified [see additional file ]., genomic trace files and est sequences from physcomitrella were examined for all plant mirnas present in mirbase (version 8.1) using microharvester []. the identified genomic, as well as est sequences, which were able to form stable hairpin-like structures were further analyzed manually. in total, a redundant set of 123 possible […]


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microHarvester institution(s)
Center for Bioinformatics Tubingen, Tubingen University, Germany; Max Planck Institute for Developmental Biology, Tubingen, Germany

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