MitoBamAnnotator pipeline

MitoBamAnnotator specifications


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


This tool is not available anymore.

Publication for MitoBamAnnotator

MitoBamAnnotator IN pipelines

PMCID: 5094714
PMID: 27812116
DOI: 10.1371/journal.pgen.1006407

[…] taking advantage of the polycistronic transcription of the mitochondrial genome [51], mtdna genomes were reconstructed from each of the rna-seq samples using mitobamannotator [52]. each reconstructed mtdna sequence underwent haplogroup assignment using haplogrep [53]. finally, multiple sequence alignment and phylogenetic analysis (neighbor joining, 1000 x […]

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 [51]., 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 […]

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

[…] (genbank accession jf317641 for “south” and jf317642 for “north” chameleons, respectively). we then converted the sam file into a sorted bam file using samtools (li et al. 2009). finally, we used mitobamannotator (zhidkov et al. 2011) to extract the entire mtdna sequence consensus from each sample. mega 6.0 (tamura et al. 2013) was used to align reconstructed mtdna genomes along […]

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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