MicroFamily
for LINUX and Windows
Emese Meglécz
IMBE, CASE 36, Aix-Marseille University, 3 place Victor Hugo, F-13331
Marseille Cedex 3, France
emese.meglecz(at)imbe.fr
Meglécz, E. 2007. MicroFamily: A computer program for
detecting flanking region similarities among different microsatellite
loci. Molecular Ecology Notes 7 : 18-20. LINK
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Overview | ||||
Microsatellite flanking regions
are not necessarily unique sequences, but they may group into sequence
families. This phenomenon seems to be widespread in Lepidoptera and also
occurs in many other insect species (Meglécz et al. 2004).
These microsatellites are likely to give multiple banding patterns during
PCR amplifications, which can be very difficult to interpret. Therefore,
identifying sequences that cluster together prior to primer design can
save considerable time and money. The flanking regions of clean microsatellite-containing sequences are then compared by an all-against-all BLASTn analysis. The E-value can be specified by the user. Sequences are sorted into four categories based on the results of the BLASTn. They are classified as (i) Unique if no similarities were observed to any other sequences of the same dataset, (ii) Redundant, if the identity to another sequence was higher than 95% along the whole flanking sequence or (iii) UnBLASTable if the sequence had no hits at all (i.e. no significant similarity to any sequences), not even with itself. This is the case if the flanking region is too short or semi-repetitive (resembles to a microsatellite but there are not enough uninterrupted repeats). All non-redundant sequences that produced a significant hit with at least one different sequence were classified as (iv) Grouped. |
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Installation of the program | ||||
The MicroFamily is written in Perl and runs under Linux or Windows. It is a collection of small programs/modules, which use the following freely available programs: | ||||
Perl (ActivePerl 5.8.7.815)Download fromhttp://www.activestate.com/Products/activeperl/index.mhtml |
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BLASTN-2.2.13Download from
ftp://ftp.ncbi.nih.gov/blast/executables/or from
http://www.ncbi.nih.gov/BLAST/download.shtml |
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CLUSTALw1.83Higgins DG, Bleasby AJ, Fuchs R (1991) CLUSTAL V: improved software for multiple sequence alignment. Cabios, 8, 189-191. |
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Start by downloading and installing the above mentioned three programs. If you have a slightly older or newer version already on you computer, it will probably not cause any problem. Then download and unzip the appropriate MicroFamily zipped folder. Detailed instructions on the use of the program are found in the README file.
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Windows
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Linux
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New version (1.2, 27 June 2008) MicroFamily (822 ko) Readme (64 ko) |
New version (1.2, 27 June 2008) MicroFamily (845 ko) Readme (59 ko) |
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Former version (16 July 2006) MicroFamily (820 ko) Readme (63
ko) |
Former version (16 July 2006) MicroFamily (796 ko) Readme (58 ko) |
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Last updated 7 october 2013 by Emese Meglécz