Wednesday, August 28, 2013

My mt-DNA Tree

My mt-DNA Tree allows you to mark the mtDNA markers on the mt-DNA-tree. It is helpful to understand how your markers fit on the tree.

Prerequisites: Microsoft .Net Framework 4.0

Usage: Just double click on it, paste your mt-DNA markers on the textbox provided and click 'Mark on Tree'.

Screenshot:

Download : MyMtDNATree.exe (335 Kb)

Source Code at GitHub.

Acknowledgements / References
Change Log
Version 1.0
  • Initial release. mtDNA tree Build 15 (30 Sep 2012)

Sunday, August 25, 2013

mtDNA Map


This tool is replaced by FASTA to RSRS (with Visualizer).


mtDNA Map is a visual representation of comparing two mtDNA fasta files. This is an easy way to see what mutations have occurred. A picture is worth a thousand words. Hence this visualization tool.

Prerequisites: Microsoft .Net Framework 4.0

Usage: Open a mtDNA file or click load RSRS. This will be the base. Then open Overlap mtDNA file which will show places where mutations/changes have occurred.

Download from Google Drive.

Change Log
Version 1.0
  • Initial Release.

Wednesday, August 14, 2013

Denisova DNA

The genome sequence of a Denisovan individual was generated from a small fragment of a finger bone discovered in Denisova Cave in southern Siberia in 2008. Approximately 30-fold coverage of the genome was generated using the Illumina GAIIx sequencing platform.

This project aims to convert the massive amount of data of Denisovan Genome to a raw data download file if FTDNA (or) 23andMe did the test. So, basically, I am just extracting the SNPs from Denisovan Genome and constructing the autosomal raw data file. This project is aimed to be more like factoids provided by FTDNA, just doing it from a hobbyist research perspective (and may produce scientific results). So, if you have a long strand/segment match which suggests that you are a cousin to Denisovan, don't blame me ;). The source files are taken from Denisovan DNA in VCF format. I used 2 laptops running 24/7 for nearly 2 weeks to parse ~ 1 terrabyte of Denisovan genome to produce the below results.

Download: 
  • GEDMatch# F999903 (FTDNA SNPs)
  • Download from Google Drive.
License:
The download pages in Max-Planck-Gesellschaft mentions: When using this genome data please cite the following publication:
Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prufer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andres AM, Eichler EE, Slatkin M, Reich D, Kelso J, Paabo S: A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science. Aug 31 2012.

References / Data Used

Tuesday, August 6, 2013

DNA Error Fix

Several people do DNA tests with multiple DNA companies. While results in general are same, a few test errors and no-calls can be fixed for the same SNP. This tool attempts to fix errors and no-calls comparing multiple DNA files of the same person tested through different companies. The file formats supported are FTDNA, 23andMe and Ancestry DNA

Prerequisites: Microsoft .Net Framework 4.0

Usage: Select the files and click Fix button. Just as a tip, hold ctrl-key when selecting for selection of multiple files (or just drag and drop over the pane).

Screenshot:

Download : DNAErrorFix.exe (51 Kb)

Source Code at GitHub.

License: The MIT License

Change Log
Version 1.6
  • Removed unnecessary no-calls in consolidated file.
Version 1.5
  • Option to choose gender to improve accuracy, esp., for X chromosome.
Version 1.4
  • FamilyTreeDNA autosomal files no calls represented as '0' chromosome causes the software to stall - fixed
Version 1.3
  • Replaces phased files - fixed
Version 1.2
  • Minor bug-fixes, consolidated file and support for decodeme.
Version 1.1
  • Converted the command-line to have a friendly user interface.
Version 1.0
  • Initial release. Supports FTDNA, 23andMe and Ancestry DNA

Altai Neanderthal DNA

The Neanderthal genome project is a collaboration of scientists coordinated by the Max Planck Institute for Evolutionary Anthropology in Germany and 454 Life Sciences in the United States to sequence the Neanderthal genome.

This project aims to convert the massive amount of data of Neanderthal Genome to a raw data download file if FTDNA (or) 23andMe did the test. So, basically, I am just extracting the SNPs from Neanderthal Genome and constructing the autosomal raw data file. This project is aimed to be more like factoids provided by FTDNA, just doing it from a hobbyist research perspective (and may produce scientific results). So, if you have a long strand/segment match which suggests that you are a cousin to Neanderthal, don't blame me ;).

Download: 
  • GEDMatch# F999902 (FTDNA SNPs)
  • Download from Google Drive.
License:
Use of the genome sequence data section in Department of Evolutionary Genetics reads,
All data is made freely available. However, we ask users to observe the Ft. Lauderdale principles, which entitles the data producers to make the first presentation and publish the first genome-wide analysis of the data. The data can be used freely for studies of individual genes or other individual features of the genome.
I am using it for hobby, so I think I don't fall under that category.

References / Data Used