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EuMicroSat db (Eukaryotic Microsatellite Database)

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

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EuMicroSat db (Eukaryotic Microsatellite Database)

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  1. EuMicroSatdb(Eukaryotic Microsatellite Database) Guru Gobind Singh Indraprastha University, Delhi 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 Genomics8(1):225 Published on (10 July 2007) http://ipu.ac.in/usbt/EuMicroSatdb.htm

  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 (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

  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 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)

  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 EuMicroSatdb also provides 200bp upstream and downstream flanking sequences of the extracted microsatellite to design primers 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. Output * indicates that (CT)12 can also be read as a (TC)12

  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 4-1-1-1 to 4-1-1-5 and the second from 4-1-1-8 to 4-1-1-10)

  37. 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

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