MitoWheel Manual

Last updated: April 6th, 2008

1. 1.Navigation
   1.1 Moving fast
   1.2 Fine navigation
   1.3 Walking through multiple matches
   

2. 2.Info box
   

3. 3.Queries
   3.1 Nucleotide positions
   3.2 Displaying mutations
   3.3 Regions
   3.4 Genes and sequence features
   3.5 Sequence motifs
   3.6 Grouping database sequences
   

1. 1.Navigation
   
   1.1 Moving fast
   The easiest way to change your position fast on the wheel is to click on it and drag it with the mouse. You also can scan through the genome by pressing the white arrowhead buttons in the sequence bar. The wheel and the sequence bar will start moving slowly then they will speed up. This way you can make fine movements by pressing the buttons briefly, and reach distant regions fast by holding down the buttons longer. If you do not hold down the buttons, but just click on them, the neighbouring nucleotide will move to the center. Pressing the left and right keys on your keyboard will produce exactly the same behaviour. (However, the fast scan will not function in FireFox when using the keyboard.) If you would like to move to a specific position, click in the search box, type in the number of the position (a number between 1 and 16569), and press ENTER.
   
   1.2 Fine navigation
   You can step to the next nucleotide position by clicking on the white arrowhead buttons in the sequence bar, or pressing briefly the left or right keys on your keyboard. You can also click on a nucleotide in the sequence bar, which will make the nucleotide move to the center. This is the ideal way to walk through a small region of the sequence: click repeatedly on a nucleotide on the side.
   
                                                           [Watch the video here]
   
   
   1.3 Walking through multiple matches
   Some of your queries might result in multiple matches. In this case the matching positions will be indicated by arrowheads around the wheel. You can make the wheel turn from one position to the other by pressing ENTER again and again. Alternatively, you can press the red arrowhead button that appears in the search box. If you hold down the SHIFT key while pressing ENTER or clicking the red arrowhead button, the wheel will move to the opposite direction. If you want to move to a matching position that is located further away, use one of the alternatives of fast moving (dragging the wheel, pressing the white arrowhead buttons in the sequence bar, or pressing the left or right keys on your keyboard). Once you are close to position that you would like to see, press ENTER (or click the red arrowhead button) and the wheel will move the exact postion.
   
   

2. 2.Info box
   Whenever the wheel stops at a site, the info box will pop up to show information about the specific nucleotide position. Next to the number showing the position, you might find a set of other numbers in parentheses. These numbers indicate how many human sequences carry a specific allele at the given position. If you were searching for a mutation, something like this will appear: ‘(5/3201)’. This means that out of the 3201 human mitochondrial DNA sequences deposited till date in databanks 5 carry the mutation that you were searching for.
   
   If you were searching for a region between two positions or a gene on the mitochondrial genome, both the start and the stop positions will be shown, and a small icon will appear in the upper right corner of the info box. Clicking on the icon you can send the nucleotide sequence of the shown region to the clipboard of your operating system. You can then easily paste the sequence to any other application running on your computer.
   
   

3. 3.Queries
   The most important feature of the MitoWheel is its versatile search function. To make a query, simply click the search box in the upper left corner, type in some term, and press ENTER. The search function is designed to be rather flexible. There are very few constrictions concerning the syntax. One of them is that multiple queries has to be separated by commas.
   
   3.1 Nucleotide positions
   If you want to find a specific nucleotide position on the human mitochondrial genome, type the number of the position (something between 1 and 16569) in the search box and press ENTER. The wheel will turn to the given position and the info box will appear with detailed information about the site. You can also see more positions at the same time if you type in several position numbers separated by commas. In this case red arrowheads will show the matching positions, and you can walk through the matches by pressing ENTER or clicking on the red arrowhead button in the search box again and again.
   
   3.2 Displaying mutations
   You can type in the search box mutation names. The wheel will behave pretty much like in case of nucleotide positions, except that additional information will be shown in the info box about the possible functional effects of the mutation. You can use several ways to describe a mutation. The simplest is to give the position followed by the mutated nucleotide: ‘12276A’. (The search is not case sensitive, so you can type ‘12276a’, as well.) Alternatively, use one of the following terms: ‘G12276A’, ‘12276G>A’, or ‘m.12276G>A’ (the latter one is the official way to describe mitochondrial sequence variations). Similar to nucleotide positions, you can see several mutations at the same time, and you can walk through them.
   
   3.3 Regions
   If you type two positions separated by a hyphen, they will be recognized as starting and ending positions of a region. If you want to switch the orientation of the region type ‘reverse’ or ‘rev’. The selected region will be shown as an arc, and the wheel will move to the starting position. By pressing ENTER or clicking the red arrowhead button in the search box, you can move to the other end, and then back again. You can save the nucleotide sequence of the selected region by clicking the small icon appearing in the upper right corner of the info box. This will send the sequence to the clipboard, from where then you can paste it to any other application. If you are at the end position of the region, the MitoWheel will send the reverse complementary sequence to the clipboard.
   
                                                          [Watch the video here]
   
   3.4 Genes and sequence features
   Using the search box, you can easily find genes and other sequence features on the human mitochondrial DNA. The most relevant loci are already indicated on the wheel, so you can use those labels to begin with your queries. However, the MitoWheel will recognize many other terms, too. As an example, any of the following terms will lead to the alanyl-tRNA: ‘A’, ‘Ala’, ‘alanine’, ‘tRNA-Ala’, ‘alanyl-tRNA’, ‘Ala-tRNA’, ‘MT-TA’, ‘transfer RNA alanine’. Apart from single genes, you can search for a group of genes, too. You might want, for example, all tRNA genes to be marked on the genome. For this, type ‘tRNA’ or ‘transfer RNA’. As in any other queries with multiple results, individual matches will be shown by arrowheads, through which you can walk with the ENTER key or the red arrowhead button in the search box. (To move to the opposite direction hold down the SHIFT key.)
   
   It is also possible to show several groups of genes at the same time. Try ‘tRNA, rRNA, protein’ as an example. You will see all 22 tRNA genes marked by red arrowheads, both rRNA genes by blue and all 13 protein coding genes by yellow arcs. (The tRNA genes are so small that it does not make sense to show them as regions.) As another example, you can see the protein coding genes grouped by protein complexes that they are part of. Type ‘complex I, complex III, complex IV, complex V’ or simply ‘c1, c3, c4, c5’. (Alternatively, you can also type ‘NADH dehydrogenase, cytochrome b, cytochrome c oxidase, ATP synthase’, but it will take much longer. If you need a reminder, which color stands for which search term, take a look at the lower left corner. There you will find the key for each color.
   
   Similar to any other regions, you can copy the sequence of any marked gene to the clipboard by stepping to the starting position of the gene and clicking on the small icon in the upper right corner of the info box.
   
   3.5 Sequence motifs
   If you would like to see whether a certain nucleotide sequence is present in the human mitochondrial genome or not, type or paste the sequence in the search box and press ENTER. If the sequence motiv can be found in the Cambridge reference sequence, the wheel will move to the starting position, and the info box will display the starting and the end positions and the orientation of the sequence. If your sequence cannot be found in the reference sequence, the query will disappear from the search box, the wheel will not move, and the info box will not pop up. It might also happen that your search gives multiple results. In this case, you will see all the matches marked by arrowheads, and you can walk through them with the ENTER key or the red arrowhead button in the search box. The query sequences has to be at least 3 nucleotide long. You can also type in multiple sequence motifs separated by commas.
   
                                                          [Watch the video here]
   
   3.6 Grouping database sequences
   The MitoWheel incorporates all complete human mitochondrial DNA sequences that were present in the GenBank database at the time of the last update. For each database sequence, you can display the differences from the revised Cambridge reference sequence by typing the GenBank accession number in the search box. More importantly, you can group the database sequences by presence or absence of specific mutations, and display mutation spectra within such groups. This can be a useful tool to explore the phylogenetic relationships between human mitochondrial DNA sequences.
   
   You can define a group of sequences by using mutation names with one of the following prefixes: ‘+’, ‘*’, or ‘-’. Sequences will be included in the group if they carry all mutations labelled with ‘plus’. Sequences will be also included if they carry at least one of the mutations labelled with ‘star’. Sequences carrying any of the mutations with ‘minus’ will be excluded.
   
   The output screen will show the complete set of mutations occurring in the defined group. Mutations present in only few sequences will appear faint, while those present in many of the selected sequences will have a bright color. The mutations are divided into four categories, and these categories are distinguished by color. ‘Specific’ mutations occur only in the selected sequences, and they cannot be found in any other human mitochondrial sequence outside of the investigated group. ‘Ubiquitous’ mutations are present in all selected sequences and some other sequences, too. These mutations often represent supergroup specific mutations. ‘Subgroup’ mutations are present only in a subset of the selected sequences, but they can also be found in sequences outside of the group. At last, the presence or the absence of some reference sequence specific mutations is shown under the category ‘rCRS’. The revised Cambridge reference sequence carries some rare polymorphisms that are actually present only in the minority of the human sequences. In such cases, the presence of the ‘mutation’ (i.e. a difference in comparison to the reference sequence) is less informative than the absence of the ‘mutation’ (i.e. the fact that the site is identical to the reference sequence).
   
   Similar to any other queries with multiple results, you can walk through the mutations that are shown in the group view. Use the ENTER key or the red arrowhead button in the search box to step between mutations, and hold down the SHIFT key if you want to move to the opposite direction. When the wheel stops at a specific position, the info box will pop up with detailed information about the mutation. Additionally, two pairs of numbers will appear next to the name of the mutation (something like this: ‘(12/50 : 12/3201)’. The first two numbers show how many sequences carry the mutation within the selected group (in this case 12 out of 50), while the second pair of numbers describes the frequency of the mutation in the entire set of human sequences. In the given example, both in the group and in the complete set there are 12 sequences carrying the mutations. This means that the mutations is specific for a subgroup of the displayed group.