Download presentation
Presentation is loading. Please wait.
Published byJermaine Batson Modified over 9 years ago
1
EuMicroSat db (Eukaryotic Microsatellite Database) How to use EuMicroSat db Guru Gobind Singh Indraprastha University, Delhi http://ipu.ac.in/usbt/EuMicroSat 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 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 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 http://ipu.ac.in/usbt/EuMicroSatdb.htmhttp://ipu.ac.in/usbt/EuMicroSatdb.htm
Similar presentations
© 2024 SlidePlayer.com Inc.
All rights reserved.