Phobos is a highly accurate and fast search tool for
Phobos - a tandem repeat search tool for complete genomes -
Version 3.3.12 is now available (September 2010) - Geneious plugin needs version 3.3.10 or higher.
New Linux binaries have been added in September 2017.
- DNA-minisatellites and
Two of our recent papers that use Phobos:
Leese, F, Mayer, C, and Held, C (2008): Isolation of microsatellites from unknown genomes using known
genomes as enrichment templates. Limnology and Oceanography: Methods 7, 412-426. (Abstract)
Mayer C, Leese F, Tollrian R (2010): Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach. BMC Genomics
Read, B.A. et al. 2013. Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499, 209-213. doi:10.1038/nature12221
Mock, T. et al. 2017. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature 541, 536-540. doi:10.1038/nature20803
Is Phobos still maintained and supported? Yes!
Phobos is a multi platform program (Mac, Linux, Windows, and maybe others, such as Solaris, upon request)
The last major version appeared in September 2010 and users might ask: Is Phobos still maintained and supported? Yes. There have been no bug reports
for a long long time. This is good news for all users.
I still intend to improve the main algorithm to make it even faster. But my time is limited and it won't be in the very near future.
For 99.9% of the users speed is no problem anyway.
If you have problems or if, unexpectedly, you discover a bug, please contact me!
that comes in two versions:
- user friendly GUI (graphical user interface) program
- easily scriptable CL (command-line) program.
Visualisation of tandem repeats and user friendly primer design
Phobos has been integrated into the following molecular biology analysis tools,
which in particular offer a convenient interfaces for designing flanking primers of microsatellites.
Commercial users always need to obtain a user license for Phobos directly from the author Christoph Mayer.
Phobos has the following main features:
STAMP: Microsatellite marker design extension for the Staden package
Kraemer, L., Beszteri, B., Gaebler-Schwarz, S., Held, C., Leese, F., Mayer, C., Poehlmann, K. & Frickenhaus, S. (2009)
STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
BMC Bioinformatics 10:41.
Phobos plugin for Geneious.
Geneious is a commercial and easy to use DNA and protein sequence analysis tool.
In order to use the tandem repeat detection capabilities of Phobos in Geneious one has to install
the command-line version of Phobos (version 3.3.10 or higher) as well as the
it uses an exact, in particular non-probabilistic search algorithm,
it can search for perfect satellites with a pattern size of 1 - 10000 bp in complete genomes,
it can search for imperfect satellites in complete genomes in the pattern size range 1 - 50 bp with a high detection and alignment quality,
and for patterns with a size of 10000 bp with a reduced detection and alignment quality.
it uses the alignment score as an optimality criterion to decide whether to extend a satellite up or downstream,
it detects and reports overlapping satellites,
it tries to extend satellites up and down stream to obtain highly accurate results which are mostly
independent of the search direction,
it is able to find alternative alignments with different units for the same satellite,
it can report repeats in a variety of different output formats, including formats that show flanking regions or
the alignment of the repeat region with the repeat pattern.
When developing a DNA-satellite search tool, two main problems occur:
The program should
(1) detect imperfect repeats, i.e. repeats with mismatches and indels,
(2) be able to cope with repeats that can be aligned with several different unit patterns.
Whereas most programs focus on problem (1), problem (2) has - to my knowledge - only been solved in the
Tandem Repeat Finder, which however uses a probabilistic, i.e. non-exact search algorithm.
Phobos has been designed to solve problems (1) and (2).
Phobos is still in development. However, since it is more accurate and more efficient than other
search tools for tandem repeats that use an exact search algorithm, it has now been made available to the public.
Currently, I am working on the following improvements:
- a better filter for reporting alternative alignments
- detection of compound satellites
Phobos is in use since the end of 2006:
- it has been used to detect tandem repeats in three genome projects now
How to cite Phobos:
Mayer, Christoph, Phobos 3.3.11, 2006-2010,
If you are using the STAMP-module of the Staden-package, please also cite:
Kraemer, L., Beszteri, B., Gaebler-Schwarz, S., Held, C., Leese, F., Mayer, C.,
Poehlmann, K. & Frickenhaus, S. (2009)
STAMP: Extensions to the STADEN sequence analysis package for high throughput
interactive microsatellite marker design.
BMC Bioinformatics 10:41.
This program Phobos is copyright protected. It is only distributed from the authors web page.
For academic and non-commercial usage this program can be used free of charge. Results obtained
with this program can be published
without restrictions, provided the program and its author are acknowledged by name.
A commercial license for Phobos can be obtained from the author.
I would like to thank the following collegues for helpful conversations and support:
Florian Leese, AWI Bremerhaven
Christoph Held, AWI Bremerhaven
Bank Beszteri, AWI Bremerhaven
Stephan Frickenhaus, AWI Bremerhaven