MitoBamAnnotator protocols

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MitoBamAnnotator specifications

Information


Unique identifier OMICS_12340
Name MitoBamAnnotator
Interface Web user interface
Restrictions to use None
Input data BAM files
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publication for MitoBamAnnotator

MitoBamAnnotator in pipelines

 (3)
2016
PMCID: 5094714
PMID: 27812116
DOI: 10.1371/journal.pgen.1006407

[…] taking advantage of the polycistronic transcription of the mitochondrial genome [], mtdna genomes were reconstructed from each of the rna-seq samples using mitobamannotator []. each reconstructed mtdna sequence underwent haplogroup assignment using haplogrep []. finally, multiple sequence alignment and phylogenetic analysis (neighbor joining, 1000 x […]

2015
PMCID: 4454688
PMID: 26039092
DOI: 10.1371/journal.pgen.1005241

[…] that aligned to the mitochondrial genome relative to the nuclear genome was calculated. using samtools, the mitochondrial reads were extracted from the bam files and analyzed with the online tool mitobamannotator []., an additional 38 te samples underwent ngs analysis in order for chromosome constitution assessment and mtdna quantification to take place. a different type of ngs technology […]

2015
PMCID: 4700957
PMID: 26590214
DOI: 10.1093/gbe/evv226

[…] sequences (genbank accession jf317641 for “south” and jf317642 for “north” chameleons, respectively). we then converted the sam file into a sorted bam file using samtools (). finally, we used mitobamannotator () to extract the entire mtdna sequence consensus from each sample. mega 6.0 () was used to align reconstructed mtdna genomes along with previously published seven whole mtdna […]


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MitoBamAnnotator in publications

 (3)
PMCID: 5123245
PMID: 28185569
DOI: 10.1186/s12859-016-1193-4

[…] for mtdna analysis, were used to provide annotations for three mitochondrial mutations involving genes coding for an rrna, a trna and a protein, respectively. web-based versions of mit-o-matic [], mitobamannotator [] and mitimpact 2.0 [] tools were also applied to the same mutations to compare their performance in variant annotation., gbrowse instance at mseqdr website [] allows visualization […]

PMCID: 4218962
PMID: 25334030
DOI: 10.1038/ncomms6257

[…] the ratio of x- to y-chromosome reads following the study by skoglund et al. (, ). samples were mapped to the mtdna genome and filtered as above. bam files were analyzed with the online tool mitobamannotator (). haplogroups were obtained with haplogrep based on the build 15 phylogeny of phylotree ()., y-chromosome haplogroups were determined for all male samples by analyzing the filtered […]

PMCID: 4125989
PMID: 25104065
DOI: 10.1038/srep05994

[…] reads to minimize the effect of deamination and sequencing errors. reads were aligned to the revised cambridge reference sequence (rcrs) and filtered as above. the final bam file was uploaded to mitobamannotator which identifies mtdna mutations which are then analysed with haplogrep identifying the most likely haplogroup to which a sample belongs., r.m., d.b. and r.p. conceived and designed […]


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MitoBamAnnotator institution(s)
National Institute for Biotechonology in the Negev, Beer Sheva, Israel; Department Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel; Shraga Segal Department Microbiology and Immunology, Ben Gurion University of the Negev, Beer Sheva, Israel

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