SRS- Sequence Retrieval System Version 7.1
General
SRS is a system to extract information from different databases and to link information present in different databases.
1. Getting started
- Please download the User Manual (PLEASE do NOT PRINT!!)
- Go to the EBI homepage http://www.ebi.ac.uk/
- Go to the Bioinformatics Products and services page
- Search and Click the SRS button
- This link will automatically Start a temporary project. (You can also start Permanent Projects but that is the subject of a longer tutorial)
- You arrive at the Quick Search page.
2. Looking for a sequence with known accesion number
- We are going to look for human glial fibrillary acidic (GFAP) mRNA,
Acc. No: J04569 in the databases EMBL.
- Selection of the databases:
show all
Tag databases, select EMBL
- Quick Search for Acc. No.: J04569
Results
- We get the sequence from the database. Click on name.
- General information.The information provided is linked to other databases, we will follow several of them.
Click on Cross-references
- MEDLINE: gets publications.
-GOA: Gene Ontology
- GDB (Genome Database in support of the Human Genome Project): lots of information
- UNI-PROT/swissProt: lots of information related to the protein sequence
Check FEATURES.
- TAXONOMY: You can walk through the taxonomic tree.
Taxon is human.
PARENT ID to go up one taxon, >>>primates (use view taxonomy)
GC ID to view Genetic Code
MGC ID to view Mitochondrial Genetic Code
3- Searching with a name on Quick search and selecting library.
Now search with the name GFAP. Check EMBL.
First use the Quick Text Search. Type GFAP.
What happens? How many entries? Can you easily find the correct sequence (J04569!!) (we make the assumption that you do not have the accesion number)?
Try to find the correct one.
Finally!
3- Advanced Query
Use Advanced query! (select EMBL again , we want only well characterized mRNA, and no so called similar to sequences!)
Click on extended query form.
You can use &, |, !
& = and
| = or (alt + 7 on MacOSX)
! = but not
Try to use the division choice.
Could you clean out the result list?
Exercise:
Isolate the GFAP mRNA of 6 species. Explain how you did.
You intend to do some expression vectors to microinject cells to study the overexpression of GFAP. You want only full lenght cDNAs (mRNAs). Do a list of possible candidates (can use different species)
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