Guru Gobind Singh Indraprastha University, Delhi
EuMicroSatdb
(Eukaryotic Microsatellite Database)
How to use EuMicroSatdb
Cite as :
Aishwarya V., Grover A. and Sharma P.C. (2007) EuMicroSatdb : A database for microsatellites in the
sequenced genomes of eukaryotes. BMC Genomics 8(1):225
Published on (10 July 2007)
http://ipu.ac.in/usbt/EuMicroSatdb.htm
EuMicroSatdb can be used to search for microsatellites from the any of the available
genome sequences.
Search can be made using various important parameters.
At present EuMicroSatdb has microsatellite data of the following species
EuMicroSatdb can search for both perfect and compound
(perfect) microsatellites and microsatellite clusters
Simple Microsatellite like
 (ATT)21
 (TTC)32
 (AACAT)11
Compound Microsatellites like
 (AAGA)15(GAAA)14(GGAG)6

(TCTT)18(TCCT)7(TCTT)7
Microsatellite Clusters

(AT)21ATAA(GCC)6TGAGCTAGGCGATAGCTA(GCG)12
This Demo will help to efficiently use EuMicroSatdb.
Few case studies are given to demonstrate the working of
the database
TIP : The most important thing while using the database is to mark the
correct checkbox. This is important as results may differ if illogical
checks and entries are made.
Searching Parameters


Repeat Unit Length (mono-, di-, tri-, tetra-, penta-,
hexa-)
Repeat Sequence
The sequence of the microsatellite e.g. GCC

Repeat No.
(AT)10 has a repeat number 10

Microsatellite Length
(ATT)20 has a motif length 60

Position
Where the microsatellite is located on the chromosome)

Interruption Size (Microsatellite Cluster)
(Difference between two adjacent microsatellites)
All the Case Studies pertain to chromosome
1 of Homo sapiens but same pattern may
be followed for rest of database
Perfect microsatellite Searching
You can search a microsatellite for any
desired sequence
Case Study 1
(Perfect microsatellite)
If you want to search for a simple pentanucleotide repeat
microsatellite with tandem repeat GGTTT, microsatellite
length greater than 210
To search for such microsatellite, use the following vaules.
TIP : The most important thing while using the database is to mark the
correct checkbox. This is important as results may differ if ill logical
checks and entries are made.
Input
Output
Flanking Sequences
EuMicroSatdb also provides 200bp upstream and
downstream flanking sequences of the extracted
microsatellite to design primers
The output of which is as follows
Case Study 2
(Perfect microsatellite)
If you want to search for all the simple
trinucleotide microsatellites in a particular
region of the chromosome…
Input
Output
Case Study 3
(undefined perfect microsatellite)
If you want to search for the a particular
trinucleotide repeat e.g. TTC whose repeat
number is greater than 50
Input
Output
If you want to search for all the microsatellites
present on the chromosome in one go, use
these values
Input
Output
For searching compound
microsatellites, search parameters are
as follows
Case Study 5
(compound microsatellite)
If you want to search for the compoud
microsatellite with a Tetra-Tetra-Tetra
combination, with the microsatellite length
greater than 100 bp
Input
Output
Case Study 6
(compound microsatellite)
If you want to search for the a compoud
microsatellite with a GTGC-CTTC-CCTC
combination, with microsatellite between
100 and 150
Input
Output
Case Study 7
(compound microsatellite)
If you want to search for the a compoud
microsatellite with a combination TTTCTCTT-TC, with the fourth association being
a tetra- and fifth being a di- repeat
(sequence unspecified) and microsatellite
length greater than 100.
Input
Output
* indicates that (CT)12 can also be read as a (TC)12
Case Study 8
(compound microsatellite)
If you want to search for a microsatellite with
a tri combination, GAA-AAG-AAC, with
repeat number more than 5 for GAA and
more than 5 for AAC (suppose you do not
know the repeat number for AAG)
Input
Output
Case Study 9
(Imperfect microsatellite)
To search for imperfect microsatellites you
have to input the interruption value i.e.
the desired number of basepair difference
between any two microsatellites
Input
Output
(The output represents two clusters (imperfect microsatellites) one
from 4-1-1-1 to 4-1-1-5 and the second from 4-1-1-8 to 4-1-1-10)
Thank you for taking the Demo
EuMicroSatdb team hopes that this demo will help you to
efficiently use this database.
If any query still persists please write to us
http://ipu.ac.in/usbt/EuMicroSatdb.htm