Getting started with a candidate gene approach

UAG - Stop and Reflect

You are interested in finding the Chamaecrista gene that is homologous to the flowering time (FT) gene in Arabidopsis. Would you use the mRNA/cDNA Arabidopsis sequence or the predicted amino acid sequence for that Arabidopsis sequence in your search? Why? Respond in your journal


UAG - Stop and Reflect

You decide to translate a cDNA sequence into a peptide sequence. What would you need to consider in predicting the peptide sequence? Respond in your journal


Once you have your sequence(s) you're ready to use BLAST

BLAST Strategies

Blast Screen Shot
Basic BLASTing in 3 easy steps



Give it a try

Here are two text files you can use to practice BLASTing at the public sites and our local Chamaecrista site. The first FASTA file is for the Arabidopsis FT (Text File 966bytes Jan19 09) sequence and the second is for a number of Arabidopsis shoot genes (Text File 301kB Jan19 09). See what happens when you BLAST a whole bunch of files at one time.

You'll probably want some more information to interpret how similar sequences are that you obtain in your BLAST search. Check out NCBI for details.