Archive for the ‘Javascript’ Category

Link to MitoWheel

May 12, 2016

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

April 5, 2016

MitoWheel was updated on April 5th, 2016.

WheelIconWell, 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!