Archive for March, 2008

A Little Make-Up

March 30, 2008

The MitoWheel was updated on March 30th, 2008. This time new: 

  1. After a few years of hesitation, I finally switched the orientations of the two replication origins. If you prefer the previous version, or you find some evidence that the previous version was more correct, please let me know.
  2. Now you can really spin the Wheel directly! Just click on it and drag it around.

Sequence Bar with Allele Frequencies

March 23, 2008

The MitoWheel was updated on 23th March, 2008. This time new:

The sequence bar now contains information not only about the function of specific nucleotides, but also about allele frequencies at polymorphic positions. Each little gray bar above or below a nucleotide letter represents the number of individuals who carry a difference  (also known as SNP) at the given position as compared to the revised Cambridge reference sequence. To be able to show both very rare and very frequent polymorphisms, the bars have a logarithmic scale.mitowheel-poly.pngI hope you will find this new feature useful. This can help you to design reliable PCR primers for the human mitochondrial genome. After all, you don’t want your primer’s 3′-end sitting right on a very frequent polymorphism (risking that under certain conditions you will not be able to amplify a PCR fragment from a subset of individuals). The allele frequency bars are also good starting points if you want to explore the diversity of the human population by using the “+” and “-” operators in the search box (as described here).

March 15, 2008

If you tried to use the MitoWheel in the last two days, you might have noticed that the site was down. I am very sorry for the inconvenience. The hosting server had serious technical problems. Well, those problems are still not solved, but in the meantime I changed provider. And if I already had to change, I used the opportunity to create a new domain. Let me introduce you the new home of MitoWheel:

The old address is supposed to work again very soon. However, after a few weeks of transition I will discontinue with it, and will be the only place to find the MitoWheel. So don’t forget to change your bookmarks. If you notice any technical issues, please report it to me.

Have fun spinning the Wheel! 

MitoWheel 1.2: Humankind in the Wheel

March 9, 2008

… or at least those individuals whose complete mitochondrial DNA sequence can be found in GenBank. MitoWheel was updated on March 8, 2008. New features:

  1. MitoWheel incorporates now data on fully sequenced human mitochondrial genomes that have been deposited in the GenBank nucleotide database by different research groups. This means at the moment 2982 complete human mitochondrial DNA sequences. You can type the GenBank accession number into the search field and you will get the list of mutations (positions that are different from the reference sequence). Of course, you can see multiple sequences at the same time (“AY665667, DQ862537”). In this case, the sequences will be distinguished by color. Well, you might ask, who will really search for DQ862537? Probably, you are right… But don’t stop reading!
  2. MitoWheel 1.2 is able to show a number of human mitochondrial sequences as a group. In the group view, mutmitowheel-t2-3a.pngations that occur in any of the sequences in the group are divided into four classes: (a) Mutations that are specific for the group, i. e. they cannot be found in any other known human mtDNA sequence, only in the analysed group. (b) Mutations that are present in all sequences belonging to the group (“ubiquitous“), but also occur outside of the group. (c) Mutations that are missing from some of the sequences, so they define a subgroup within the group. (d) At last, the status of certain sites is shown, although they are identical to the revised Cambridge reference sequence (rCRS). It is necessary, because the reference sequence itself carries some polymorphisms that actually represent a minority within the human population. At such nucleotide positions, where sometimes 98% of the human mtDNA sequences differ from the reference sequence, the lack of the “mutation” is more informative than its presence. For the same reason, rCRS polymorphisms are faded out if they fall into the “ubiquitous” group. Color intensity gives additional information about “specific” and “subgroup” mutations too: those that are carried by many individuals in the group are shown in bright color, while rare ones are faded out. You can also find exact numbers about these features in the info window: next to the name of the mutation, frequency data are shown. The first pair of numbers says how many sequences carry the mutation within the group, and the second pair of number describes how frequent the mutation is in the entire human population.
  3. How to create groups of human sequences? By mutations! Select all sequences that carry a certain mutation, or select exactly those that lack it. You just simply have to  type a “+” or a “-” in frontmitowheel-t2-2.png of the name of the mutation. For example, “+4917G, +1888A, -12633A, -930A” means “include sequences that carry 4917G and 1888A, but lack both 12633A and 930A”. This will give a nice little group of 24 sequences with many characteristic mutations (“ubiquitous”), and a dark blue “subgroup” mutation, 11812G, that is missing only from one of the sequences (“23/24” in the info window). So why don’t you check out that subgroup by typing “+4917G, +1888A, -12633A, -930A, +11812G”? Are you aware that you are doing phylogenetics right now? You landed in a subgroup of the human T2 subclade in haplogroup T.
Navigation has been improved. When you are walking through multiple matches using the ENTER key or the red arrow in the search field, you can move to the opposite direction by holding down the SHIFT key. If you would like to move to a specific match, first spin the wheel somewhere close to the spot (using the white arrows or the arrow keys on your keyboard) and then use ENTER or SHIFT+ENTER (or the red arrow with or without SHIFT) to step to the exact position.