Tag: Mitochondrial DNA

MitoTool 1.1.2 / MitoToolPy 1.0 – Analysis of Mitochondrial DNA of eight Domestic Animals

MitoTool 1.1.2 / MitoToolPy 1.0

:: DESCRIPTION

MitoTool is a web-based bioinformatics platform, provides a convenient, user-friendly interface for handling human mtDNA sequence data.

MitoToolPy is designed for data analysis of mitochondrial DNA of eight domestic animals, including cattle, chicken, dog, horse, goat, pig, sheep and yak.

::DEVELOPER

Yao Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

MitoTool /  MitoToolPy

:: MORE INFORMATION

Citation

MitoTool: a web server for the analysis and retrieval of human mitochondrial DNA sequence variations.
Fan L, Yao YG.
Mitochondrion. 2011 Mar;11(2):351-6. doi: 10.1016/j.mito.2010.09.013. Epub 2010 Oct 7.

Mol Ecol Resour. 2015 Feb 5. doi: 10.1111/1755-0998.12386.
DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals.
Peng MS1, Fan L, Shi NN, Ning T, Yao YG, Murphy RW, Wang WZ, Zhang YP.

mtDNAmanager – Management and Quality Analysis of Mitochondrial DNA Control Region Sequences

mtDNAmanager

:: DESCRIPTION

mtDNAmanager provides a convenient web interface to analyze, query and store human mtDNA control region sequences

::DEVELOPER

Yonsei DNA Profiling Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Nov 17;9:483. doi: 10.1186/1471-2105-9-483.
mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences.
Lee HY1, Song I, Ha E, Cho SB, Yang WI, Shin KJ.

mtDNA-Server v2 – Analysis of human Mitochondrial DNA data

mtDNA-Server v2

:: DESCRIPTION

mtDNA-Server is a free mtDNA NGS analysis pipeline including heteroplasmy detection and haplogroup-based contamination deconvolution.

::DEVELOPER

GenEpi – Division of Genetic Epidemiology Innsbruck

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud.
Weissensteiner H, Forer L, Fuchsberger C, Schöpf B, Kloss-Brandstätter A, Specht G, Kronenberg F, Schönherr S.
Nucleic Acids Res. 2016 Apr 15. pii: gkw247

MitoBreak – Mitochondrial DNA Breakpoints Database

MitoBreak

:: DESCRIPTION

MitoBreak provides a complete, quality checked and regularly updated list of breakpoints from three classes of somatic mtDNA rearrangements: circular deleted (deletions), circular partially-duplicated (duplications) and linear mtDNAs.

::DEVELOPER

Filipe Pereira

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Jan 1;42(1):D1261-8. doi: 10.1093/nar/gkt982.
MitoBreak: the mitochondrial DNA breakpoints database.
Damas J, Carneiro J, Amorim A, Pereira F.

mtDNAprofiler – Mitochondrial DNA Sequence Analysis Tool

mtDNAprofiler

:: DESCRIPTION

mtDNAprofiler is a web program which enables users to analyze and compare mtDNA sequences whether they are indicated as FASTA format or as a difference to revised Cambridge Reference Sequence (rCRS).

::DEVELOPER

Yonsei DNA Profiling Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Forensic Sci. 2013 Jul;58(4):972-80. doi: 10.1111/1556-4029.12139. Epub 2013 May 17.
mtDNAprofiler: a Web application for the nomenclature and comparison of human mitochondrial DNA sequences.
Yang IS1, Lee HY, Yang WI, Shin KJ.

MitoCounter 1.0.1 – Counting mitochondrial DNA Reads from Whole Genome Sequence

MitoCounter 1.0.1

:: DESCRIPTION

MitoCounter is a tool for counting mitochondrial DNA reads from Whole Genome Sequence

::DEVELOPER

Frank Hsueh-Ting Chu

:: SCREENSHOTS

MitoCounter

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MitoCounter

:: MORE INFORMATION

Citation

BMC Genomics. 2012;13 Suppl 7:S5. doi: 10.1186/1471-2164-13-S7-S5. Epub 2012 Dec 13.
Quantitative assessment of mitochondrial DNA copies from whole genome sequencing.
Chu HT, Hsiao WW, Tsao TT, Chang CM, Liu YW, Fan CC, Lin H, Chang HH, Yeh TJ, Chen JC, Huang DM, Chen CC, Kao CY.

mtDIS – Mitochondrial DNA Distance analysis program

mtDIS

:: DESCRIPTION

MTDIS (mitochondrial DNA distance analysis program) was initially written to calculate genetic distances between populations for restriction site data obtained from single copy DNA sequences (eg. mtDNA).  The present version of MTDIS will also calculate inter-population genetic distances for DNA sequence data obtained from single copy DNA.

::DEVELOPER

Roy G. Danzmann

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MTDIS

:: MORE INFORMATION

Citation

Danzmann, R.G. 1998.
MTDIS: A computer program to estimate genetic distances among populations based upon variation in single copy DNA.
J. Hered. 89: 283-284.

MitoDis – Detection of Mitochondrial DNA mutation Involvement in Diseases

MitoDis

:: DESCRIPTION

MitoDis is intended to implement a test to detect mitochondrial DNA mutation involvement.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 MitoDis

:: MORE INFORMATION

Citation

Sun FZ, Cui J, Gavras H, and Schwartz F.
A Novel Class of Tests for the Detection of Mitochondrial DNA Mutation Involvement in Diseases.
Am. J. Hum. Genet. 72 (2003) pp. 1515-1526