Recommended to use Krait https://github.com/lmdu/krait
What is MSDB
MSDB (Microsatellite Search and Building Database) is specially designed to offer you a user-friendly interface for finding microsatellite markers, their exact position and frequency of occurrence from genomic sequence. MSDB can accept large number of sequences in GenBank, FASTA and EMBL formats as input and large number of motifs can be searched simultaneously. The program not only can search pure microsatellite but also can search compound and complex microsatellite. The outputs are Microsoft Excel statistics and SQLite database file which is convenient for analysis and classification of microsatellites. MSDB also can generate sliding window plot to show distribution of microsatellite on chromosome or sequence. The program is designed to run on Windows and Linux system as a standalone application with a user-friendly interface.
Introduction to microsatellites
Microsatellites or simple sequence repeats (SSRs) are 1-6 base pair (bp) nucleotide motifs tandemly repeated DNA sequences that are frequently distributed in eukaryotic genomes. Because of their high polymorphism, co-dominance and potential for high throughput analysis, microsatellites have been preferred as powerful tools for population biology and genetic studies in many organisms. Microsatellites can be grouped into six categories: pure microsatellite or perfect microsatellite consists of identical repeats; interrupted pure microsatellite consists of two or more individual pure microsatellite with the same motif; compound microsatellite consists of two adjacent pure microsatellites with different motifs; Interrupted compound microsatellite consists of two repetitive sequences of compound microsatellites interrupted by a short non-repetitive sequence; complex microsatellite contains several different perfect repetitive sequences; interrupted complex microsatellite contains several different perfect repetitive sequences interrupted by non-repetitive sequences.
Like most software, MSDB is distributed under a license, which means there are certain things that you are legally permitted (and not permitted) to do with MSDB software and source code. MSAE is free software and distributed under a license called the GNU General Public License (GPL http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html), a very popular license in the open source industry.
There is a full manual that contains information on running the program as a stand alone application on your own machine. The PDF version of the manual can be downloaded from http://msdb.googlecode.com/files/manual.pdf.
Though we are using this software successfully, there’s a small chance of bugs turning up somewhere. Should you find any, please contact us and we will squash them. We welcome comments and suggestions for new features or other improvements.
Lianming Du, Yuzhi Li, Xiuyue Zhang, Bisong Yue (2013) MSDB: a user-friendly program for reporting distribution and building databases of microsatellites from genome sequences. Journal of Heredity. 104(1):154-157.