Guru Gobind Singh Indraprastha University, Delhi Eu. Micro. Satdb (Eukaryotic Microsatellite Database) How to use Eu. Micro. Satdb Cite as : Aishwarya V. , Grover A. and Sharma P. C. (2007) Eu. Micro. Satdb : 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/Eu. Micro. Satdb. htm
Eu. Micro. Satdb 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 Eu. Micro. Satdb has microsatellite data of the following species
Eu. Micro. Satdb can search for both perfect and compound (perfect) microsatellites and microsatellite clusters 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 Microsatellite Clusters n (AT)21 ATAA(GCC)6 TGAGCTAGGCGATAGCTA(GCG)12
This Demo will help to efficiently use Eu. Micro. Satdb. 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 n n Repeat Unit Length (mono-, di-, tri-, tetra-, penta-, hexa) Repeat Sequence The sequence of the microsatellite e. g. GCC n Repeat No. (AT)10 has a repeat number 10 n Microsatellite Length (ATT)20 has a motif length 60 n Position Where the microsatellite is located on the chromosome) n 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 Eu. Micro. Satdb also provides 200 bp 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 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 Eu. Micro. Satdb 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/Eu. Micro. Satdb. htm
Скачать презентацию Guru Gobind Singh Indraprastha University Delhi Eu Micro
5ca669ce93e1f0818fb7ce31c71c12a8.ppt