When the wheel breaks

If you want to know what happens when the circular mitochondrial genome breaks and suddenly has two ends (aka linear), take a look at our new paper in Nature Communications. Would you ever believe that exonucleases famous for their fine sculpting abilities could be so brutal?

Link to MitoWheel

If you have a website dealing with human mitochondrial DNA and you would like to show specific positions graphically, you can now make a direct link to MitoWheel. Simply send your query through the HTML address line appending a question mark and the query text. Something like this:
http://mitowheel.org/mitowheel.html?4277C
or
http://mitowheel.org/mitowheel.html?tRNALeu

Small addition: using the left and right arrow keys on your keyboard, you can now walk through the sequence nucleotide by nucleotide. If you want to make bigger jumps, type into the search field ‘+42’ or ‘-17’ and press ENTER repeatedly.

MitoWheel 2.0

MitoWheel was updated on April 5th, 2016.

Well, it is actually more than just an update. MitoWheel has been re-made from scratch and is now fully based on Java. This means that you will be able to use it on mobile devices or some smart TVs. The actual version contains all features that I myself regularly use. Nevertheless, some functions of the old version are not yet implemented. If you cannot do without them, you will find a link on the ‘About’ page to the predecessor. This you can access by clicking on the ‘+’ sign. New is the orange button in the search field that serves for launching a query or walking through multiple matches, things that otherwise can be done by pressing ENTER. On the other end of the search field, you will find the search icon, similar to the old version. New is that you can click on it to load files with lists of queries, most importantly with lists of SNPs. The files should be simple text files in FASTA format (‘>Sequence_Name’ followed by a comma-separated list of SNPs in one or more lines) or VCF-type text files that are used to represent exome sequencing data. If you would like to use file types that do not load into MitoWheel 2.0, email me a sample, and I will do my best to extend its file reading capabilities.

Short summary of features:

• Navigate by clicking on the point of interest either on the sequence bar or on the Wheel
• If you are bored, you can just flick the sequence bar or the Wheel. You have won if it stopped in the anticodon of a tRNA (chances are 66 to 16569)
• Search for nucleotide sequence motifs, now including ambivalent positions. You can either use usual IUPAC nucleotide codes (‘R’ for ‘A’ or ‘G’, ‘Y’ for ‘C’ or ‘T’, etc.) or indicate the alternative nucleotides in square brackets (‘AC[GC][AGCT]CC[AT]GC’)
• Search for terms like ‘protein’, ‘MT-TS2’, ‘complex IV’
• If you want to search for multiple terms, separate them by comma
• Load files by clicking on the search icon
• The purple frequency bars, located below or above each nucleotide, are now calculated based on 30,181 human database sequences. Exact numbers are displayed if you search for specific alleles (‘5846C’ or ‘m.12367A>G’)

Note on privacy: Once loaded into your browser, MitoWheel 2.0 functions entirely offline. No data are sent through the net. In case some future functions will require a connection to the server, this will be explicitly indicated.

I hope you will have fun with MitoWheel 2.0. If you miss some features, either from the old version or something that just crossed your mind, do not hesitate to email me. MitoWheel is probably not free of errors. If you notice one, please let me know. Just as in the last eight years, keep the Wheel rolling!

MitoWheel and Flash Player

MitoWheel was updated on October 3rd, 2011.

A recent update of Adobe Flash Player for Mac made the allele frequency bars shifted to the left. The bars were placed somewhere between two nucleotides, and the hight of the bars did not meet allele frequency data in the info window. The problem has now been corrected. If you use an old version of Flash Player on your Mac, the correction might actually cause a shift to the right. If this is the case, please let me know (along with the version number of your Flash Player), or simply update your Flash Player.

Since this is the first update after three and a half years, I would like to thank to all users of MitoWheel. Special thanks to those who shared their opinion with me or gave some suggestions. Do not give up the hope that Mitowheel 2.0 will come some day (but then without Flash Player)! While waiting, you can read about MitoWheel in the book “The Human Genome – A User’s Guide” by Julia E. Richards and R. Scott Hawley.

MitoWheel Reloaded

The MitoWheel was updated on April 12th, 2008.

The way how the MitoWheel loads at start has been redesigned. On some computers where the loading procedure lasts longer, an error message appeared in previous versions due to time out. (Thanks to nuin for pointing out the problem.) With this update, the Flash Player message should not pop up anymore. In addition, you can also see the progress of the calculations as shown by dots in the search box. If you still have problems loading the MitoWheel, please let me know.

MitoWheel: The Manual

The MitoWheel was updated on April 6th, 2008.

There were small corrections made to the program. However, the most relevant change happened to the web site. I deleted the words ‘Under construction’ in the section ‘How to use’, and I wrote quite a lot of other words instead. Most of the instructions and tricks have been already mentioned here in the blog, but now you can find a more systematic guide right there where the Wheel is. To make the manual more enjoyable, I also included three short videos showing the Wheel in action.

 

As an appetizer, here you can see the first video about navigating the Wheel. For better quality, check out the original.

A Little Make-Up

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

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.I 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).

MitoWheel.org

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: MitoWheel.org.

The old address is supposed to work again very soon. However, after a few weeks of transition I will discontinue with it, and MitoWheel.org 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

… 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, mutations 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 front 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.

Tipp:

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.