A detailed tutorial on how to use the Database

                                                             Please take this tutorial before accessing the database    

UgMicroSatdb can be used to search for microsatellites from the Unigene sequences from 80 genomes. Search can be made using various important parameters. At present EuMicroSatdb has microsatellite data of the following species

UgMicroSatdb can search for both perfect and compound (perfect) microsatellites

 Simple Microsatellite like

n      (ATT)21

n      (TTC)32

n      (AACAT)11  

Compound Microsatellites like

n      (AAGA)15(GAAA)14(GGAG)6

n      (TCTT)18(TCCT)7(TCTT)7

This Demo will help user to efficiently use UgMicroSatdb. 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 inappropriate checks and entries are made.

Searching Parameters

 n      Repeat Unit Length

     (mono-, di-, tri-, tetra-, penta-, hexa-)

n      Repeat Sequence

     The sequence of the microsatellite e.g. GCC

n      EST/cDNA/CDS name

    Name of any particular region

n      Repeat Sequence Class

     Repeats can be extracted on the basis of the major classes

n      Amino Acid (codon repeats)

      Repeats coding for amino acids; specifying charge (basic, acidic or neutral), polarity (polar or non-polar), hydrophobicity or hydrophillicity

n      Repeat Number

    (AT)10 has a repeat number 10

n      Microsatellite Length

     The length of the microsatellite

Other features :

The Database also provides a batch Download feature to download all the results of a particular query on a single click.

Each entry is linked to the GI number clicking on which further details of the unigene sequence from NCBI can be seen.

The database also provides a link to the Primer designing tool, which can be used to design primers for the selected sequences

                                                 CASE STUDIES

All the case studies pertain to chromosome Oryza Sativa  but same pattern may be followed for rest of database

Case Study 1
(Perfect microsatellite)

If you want to search for a simple trinucleotide repeat microsatellite with tandem repeat GCA, microsatellite  length greater than 15. To search for such microsatellite, use the following vaules.

                                                                                                               Input

                                                                                        Output

Case Study 2

If you want to search for all the  trinucleotides present in a CDS, EST or cDNA region

 Input

Output  

Case Study 3
 

 If you want to search for all the  tri repeats for a particular ID [GB, GI or UG]

Input

 Output

Case Study 4

 If you want to see the presence of microsatellites in in a particular type of CDS e.g. that of a Kinase

 Input

Output

Case Study 5
 

 If you want to search for a particular class of trinucleotide repeat e.g. CCG

Input

Output

Case Study 6

If you want to search for a stretch of a particular tri repeat which codes for a particular amino acid i.e. codon repeats

  Input

Output

Feature

Similarly, specific searches can be made for codon repeats specifying charge (basic, acidic or neutral), polarity (polar or non-polar), hydrophobicity or hydrophillicity.

 
Case Study 7

If you want to search microsatellites on the basis of their length; if you want to search for microsatellites which are more than 50 bp in length

Input

Output  

Case Study 8

(Compound Microsatellite)

If you want to search for compound microsatellites on the basis of their length; if you want to search for microsatellites which are more than 50 bp in length 

Input 

 Output

Unigene Sequence

 UgMicroSatdb also provides unigene sequences of the extracted microsatellite to design primers. The output of which is as follows