Exercise 5: Motif Searches and Regular Expressions.

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Omar Harb

Monday, June 7th: 3:30 pm - 4:30 pm

5.1 Using InterPro domain searches to identify unannotated kinesin motor proteins.

Note: For this exercise use http://www.tritrypdb.org

Identify all genes annotated as hypothetical in L. braziliensis. (hint: use the full text search, and look for genes with the word "hypothetical" in their product names).

How many of these hypothetical genes have a kinesin-motor protein InterPro domain? Add and interpro domain step -- (hint: go to the interpro domain search under similarity/pattern, start typing the work kinesin, it should autocomplete).

Go to the gene page for LbrM32_V2.0490 and look at the protein feature section. Does this look like a possible motor protein?

5.2 Using regular expressions to find motifs in TriTypDB. Finding active trans-sialidases in T. cruzi.

T. cruzi has an expanded family of trans-sialidases. In fact, if you run a text search for any gene with the word "trans-sialidase", you return over 1400 genes!!! Try this and see what you get.

However, not all of these are predicted to be active. It is known that active trans-sialidases have a signature tyrosine (Y) at position 342 in their amino acid sequence. Add a motif search step to the text search in 'a' to identify only the active trans-sialidases. (hint: for your regular expression, remember that you want the first amino acid to be a methionine, followed by 340 of any amino acid, followed by a tyrosine 'Y') - refer to regular expression handout.

If you need help, you can go to this sample strategy below to see the answer: http://tritrypdb.org/tritrypdb/im.do?s=934dce48a451cbdf