Download Introduction to databases

INTRODUCTION TO DATABASES PRACTICAL
QUERY SEQUENCE
>my weird new protein
MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT
PLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC
KPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVV
HFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQG
SNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
1. DO A INTERPROSCAN
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http://www.ebi.ac.uk/Tools/services/web/toolform.
ebi?tool=iprscan using the sequence of interest
Clear all program options and then select only
‘FPrintscan’ and ‘PatternScan’ and then submit
Copy the image that is returned as the result
summary for inclusion in your report
What is the putative function based on the
patterns reported by Interpro?
NOW DO A PROTEIN BASED BLAST
SEARCH
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(http://blast.ncbi.nlm.nih.gov/Blast.cgi) using the
same sequence.
Discuss whether the results correspond with the
pattern results in terms of predicted function.
Explain why these small motifs are so
evolutionarily conserved that they can be used to
predict what a protein’s function is?
3. EXPLORE ENTREZ
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Click through the ‘G’ link in the first BLAST
result. Use as much information on the next page
and links from it (HINT: Click the ‘OMIM’ link
on the right hand side of the page) to answer the
following, with a reasonable amount of detail:
What is this protein’s function in terms of its
cellular role?
What disease(s) is it involved in when mutated?
(HINT: there is more than one – look
carefully)
4. USE THE MODEL ORGANISM DATABASES
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Use the Mouse Genome Database and check what
physiological characteristics become apparent when
the gene is experimentally disrupted:
Go to http://www.informatics.jax.org/
Click on ‘Genes’ and do a Gene & Markers query
using the gene symbol with the default settings
Scroll down to the ‘Alleles and Phenotype’ section and
click on the linked number next to ‘All alleles’
Do the experimental phenotypes agree with the
diseases you found in (3)? Explain.
Would you have been able to get a good idea of the
HUMAN gene’s cellular functions from the mouse
information if you knew completely nothing about it?
Explain.