Posts Tagged ‘mutation’

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).

MitoWheel 1.1 Goes Rainbow

February 10, 2008

The MitoWheel was updated on February 10th, 2008. New features:    

  1. You have already discovered for sure that the MitoWheel is able to show multiple results from any query. You get such multiple results if you type something like “tRNA” or “AGCTA”. You can then walk throughmitowheelcolors.jpg the results by clicking the red arrow in the search field, or simply pressing ENTER over and over. With the  MitoWheel 1.1, we are going one level higher: you can now see several lists of results at the same time. As you might guess from the title of this blog, the different groups of matches are distinguished by color. For example, you can try “complex I, complex III, complex IV, complex V” (as a matter of fact, “c1, c3, c4, c5” works as well). You will get all the mitochondrially encoded subunits of these protein complexes, each complex in another color. To find out what each color stands for, take a look at the lower left corner. The only rule to make multiple searches is: separate the terms with commas.
  2. If your search returns a region that is longer than 30 nucleotides, it will now be shown as an arc.
Tipps:
  1. Do you want to see, why the two strands of the mitochondrial DNA are called “heavy” and “light”? Type “CCC, GGG” and press ENTER. Cytosine has a molecular weight of 111.10 g/mol, while guanine 150.13 g/mol. The strand with more guanines is, therefore, heavier than the one with mainly cytosines. (Please note that most genes on the mitochondrial genome are physically located on the heavy strand. If it looks the other way around, it is because gene sequences are always given as the complementary strand that corresponds to the mRNA that is transcribed from the gene.)
  2. If you really want a lot of colors, try this: “TTTT, AAAA, CCCC, GGGG”. Then this: “I love mtDNA, TTTT, AAAA, CCCC, GGGG”, and this: “I love mtDNA, and the MitoWheel too, TTTT, AAAA, CCCC, GGGG”. (Well, you can skip the nonsense, it will be ignored anyway. But keep the extra commas to shift the color scheme.) If you make some search that turns the MitoWheel into a colorful piece of art, send me the text of the query and the title of your mito-painting. We could make a gallery…
 

Cut and Paste the Human Mitochondrial DNA

January 30, 2008

The MitoWheel was updated on January 30, 2008.  New features:

  1. Beside positions, regions, gene names, general terms, or sequence motifs, now you can type into the search field mutations too. What happens is not very different from that when you are searching for a specific position: the wheel moves to the corresponding position. The change is in the info window. If your position is in a protein coding or a tRNA coding region, you will get an additional info on the functional change caused by the mutation. Mutations are accepted in the following forms: 12276A, G12276A, 12276G>A, or if you are a perfectionist m.12276G>A.
  2. The results of your queries can be now sent to the clipboard of your operating system. If a search returns a region (i.e. more than just one nucleotide position) a small sign appears in the upper right corner of the info window. If you click on this sign, the sequence will be saved in the clipboard. You can now easily paste it into any other program.


Tipp:  If you more or less found the region on the wheel that you were searching for, and want to make some fine navigation, try the following possibilities:

  1. Click on the left or right arrows quickly.
  2. Press briefly the left or right buttons on your keyboard.
  3. Click on a nucleotide in the sequence bar. This nucleotide will move to the center.