Wednesday, 5 November 2014

BLASTing Tips

This week we have started BLASTing again in Y12 classes and by the end of the first weekly sessions, all of you will have gone through the basic steps. I walked around at the end of each session yesterday and checked that you had all worked through the CFTR primary structure search and then your own searches looking at the human h(a)emoglobin alpha chain sequence similarities across the species. I wanted to just add a reminder for the two key sites and in particular to encourage you all to sign up for an NCBI account: it will store all of your searches and will be something to show to future employers or University interviewers!

NCBI (and remember to use BLASTp)

PubMed (and remember to select Proteins, from the drop down menu)

A second tip at this stage is to add terms to refine your search. As I said a thorough grounding in classical languages helps with BLAST. So if you want to compare a sequence from man (eg Histone) add homo. If you are looking for a bacterial DNA Polymerase add coli. This will help you select the correct "hit" from the long list. Finally, check the number of amino acids in the sequence you are looking for. This is given in the summary information for each hit. So a 13 aa sequence is not likely to be correct for CFTR which is nearly 1500 aa (use wikipedia if in doubt to find more info about your query sequence). We shall continue with the introduction-search-discuss-search again sessions over the next few weeks.

Key Words BLAST, Primary structure, sequence alignment, NCBI, PubMed

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