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EuMicroSat db (Eukaryotic Microsatellite Database) How to use EuMicroSat db Guru Gobind Singh Indraprastha University, Delhi

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Presentation on theme: "EuMicroSat db (Eukaryotic Microsatellite Database) How to use EuMicroSat db Guru Gobind Singh Indraprastha University, Delhi"— Presentation transcript:

1 EuMicroSat db (Eukaryotic Microsatellite Database) How to use EuMicroSat db Guru Gobind Singh Indraprastha University, Delhi db.htm 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)

2 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

3 EuMicroSatdb can search for both perfect and compound EuMicroSatdb can search for both perfect and compound (perfect) microsatellites and microsatellite clusters (perfect) microsatellites and microsatellite clusters Simple Microsatellite like (ATT)21 (ATT)21 (TTC)32 (TTC)32 (AACAT)11 (AACAT)11 Compound Microsatellites like (AAGA)15(GAAA)14(GGAG)6 (AAGA)15(GAAA)14(GGAG)6 (TCTT)18(TCCT)7(TCTT)7 (TCTT)18(TCCT)7(TCTT)7 Microsatellite Clusters (AT)21 ATAA (GCC)6 TGAGCTAGGCGATAGCTA (GCG)12 (AT)21 ATAA (GCC)6 TGAGCTAGGCGATAGCTA (GCG)12

4 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. This Demo will help to efficiently use EuMicroSatdb. Few case studies are given to demonstrate the working of the database

5 Searching Parameters Repeat Unit Length (mono-, di-, tri-, tetra-, penta-, hexa-) Repeat Unit Length (mono-, di-, tri-, tetra-, penta-, hexa-) Repeat Sequence Repeat Sequence The sequence of the microsatellite e.g. GCC The sequence of the microsatellite e.g. GCC Repeat No. Repeat No. (AT) 10 has a repeat number 10 (AT) 10 has a repeat number 10 Microsatellite Length Microsatellite Length (ATT)20 has a motif length 60 (ATT)20 has a motif length 60 Position Position Where the microsatellite is located on the chromosome) Where the microsatellite is located on the chromosome) Interruption Size (Microsatellite Cluster) Interruption Size (Microsatellite Cluster) (Difference between two adjacent microsatellites) (Difference between two adjacent microsatellites)

6 All the Case Studies pertain to chromosome 1 of Homo sapiens but same pattern may be followed for rest of database

7 Perfect microsatellite Searching You can search a microsatellite for any desired sequence

8 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.

9 Input

10 Output

11 Flanking Sequences EuMicroSat db also provides 200bp upstream and downstream flanking sequences of the extracted microsatellite to design primers The output of which is as follows The output of which is as follows

12 Case Study 2 (Perfect microsatellite) If you want to search for all the simple trinucleotide microsatellites in a particular region of the chromosome…

13 Input

14 Output

15 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

16 Input

17 Output

18 If you want to search for all the microsatellites present on the chromosome in one go, use these values

19 Input

20 Output

21 For searching compound microsatellites, search parameters are as follows

22 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

23 Input

24 Output

25 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

26 Input

27 Output

28 Case Study 7 (compound microsatellite) If you want to search for the a compoud microsatellite with a combination TTTC- TCTT-TC, with the fourth association being a tetra- and fifth being a di- repeat (sequence unspecified) and microsatellite length greater than 100.

29 Input

30 * indicates that (CT)12 can also be read as a (TC)12 Output

31 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)

32 Input

33 Output

34 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

35 Input

36 Output (The output represents two clusters (imperfect microsatellites) one from to and the second from to )

37 Thank you for taking the Demo EuMicroSat db team hopes that this demo will help you to efficiently use this database. EuMicroSat db team hopes that this demo will help you to efficiently use this database. If any query still persists please write to us If any query still persists please write to us


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