Frequently Asked Questions

Why is MitoFun useful for my research?

MitoFun is an online resource primarily targeting scientists interested in fungal mitogenomics, phylogenetics, evolution and taxonomy. MitoFun provides the most complete collection of fully sequenced fungal mitochondrial (mt) genomes, and tools for analysis and visualization. Synteny and Blast are tools which help users extract the necessary conclusions for their own research. Finally, the ability to download sequences of all conserved genes/proteins from complete mt genomes in FASTA format, supported by relevant literature, enables further analyses.

How can I use the Genome browser?

A short MitoFun Tutorial is provided online. GBrowse provides several features, such as saving and downloading data, enlarging a small section of a genome and displaying restriction profiles. Novice GBrowse users are further assisted by the integrated online help pages.

How can I access my favorite mitochondrial genome in the Genome browser?

There are several ways to retrieve a fungal mt genome:

My favorite fungal mt genome is not listed in the phylogeny.

The fungal phylogeny provided is not necessarily in line with the complete content of MitoFun. Therefore, a few fungal mt genomes included in MitoFun are not displayed on the phylogenetic tree and vice-versa. For a comprehensive list of all complete genomes available in MitoFun select Browse -> Species List from the top MitoFun menu. We welcome feedback regarding complete fungal mt genomes which are not yet included in MitoFun.

What is the difference between the two Synteny display modes?

Both Synteny display modes provide visual aid for gene order comparisons. Synteny by blocks

Can I upload my own mt genome sequence?

Unfortunately, this is not possible at the moment. Please contact the MitoFun Team and we will add your genome sequence during the next update!

Can I download sequence data?

Yes, please visit the the top MitoFun Menu, select Overview -> Download Sequences and then choose the file(s) you want to download.

Why is not my paper cited?

We suggest several research articles for fungal mt genome analyses or related subjects, but in no way, this literature list is complete. They are proposed only as a starting point. 

How can I cite the MitoFun database?

A paper describing MitoFun is submitted for publication. Please cite: “Ntertili M., Kirmitzoglou I., Kouvelis V.N., Promponas V.J., Typas M.A. (2013). MitoFun: A Curated Resource of Complete Fungal Mitochondrial Genomes. Submitted”

Whom do I contact for providing feedback?

Any member of the MitoFun Team will be more than happy to accept your comments and will try to answer your question(s), if any.

How often is MitoFun updated?

MitoFun is a manually curated database. The MitoFun Team has decided to update the database on a regular basis, approximately 2-3 times each year. During the updates, novel manually annotated genomes may be entered, analysis tools will be added and existing annotations may be enhanced. The dates of creation and last update of any MitoFun genome entry are displayed in the Table accompanying the respective Genome Browser.

Can I provide my sequences to the MitoFun database?

We will be more than happy to receive your fungal complete mt sequence, if you wish to submit it to MitoFun database. However, have in mind that the fully annotated database will be uploaded to MitoFun website when the next update will be performed (see previous).

Contact:
The MitoFun Team welcomes suggestions, comments and submission of novel fungal mt genomes. Please feel free to contact any of the MitoFun Team Members.

Acknowledgements:
MitoFun is a collaborative project between the Department of Genetics and Biotechnology (Faculty of Biology, University of Athens) and the Bioinformatics Research Laboratory (Department of Biological Sciences, University of Cyprus).
This project was partially funded by the University of Athens (Kapodistrias grant no. 70/4/8804) and the University of Cyprus (Grant 3/311).
The MitoFun development team: Ioannis Kirmitzoglou, Maria Ntertili, Stella Tamana, Ioanna Kalvari, Michalis Vasiliadis, Vassili N. Kouvelis, Vasilis J. Promponas, and Milton A. Typas
© 2006-2013 Bioinformatics Research Laboratory, University of Cyprus
© 2006-2013 Department of Genetics and Biotechnology, University of Athens