CDS Analysis

   Once you have figured out which organism's genome your sequence (also referred to as a CDS, a Coding DNA Sequence) matches, you can analyse it. You can take the actual sequence of the organism (this will be more accurate than the one that you received from the DNA sequencing facility) and use it to do a protein BLAST. To do this, first go to http://www.bioinformatics.org/sms2. Enter the actual sequence you obtained from the BLAST and enter it on this website to translate the DNA sequence into a protein. Use all three reading frames. The different reading frames refer to how the DNA sequence can be read. Amino acids are based on three letters within the DNA sequence; therefore, there are three different ways to read the CDS. To find out which reading frame is the most accurate, find the one with the least number of asterisks (*), because each asterisk indicates a stop signal, and the protein sequence with fewer asterisks will have the longest protein. Then, take this sequence (the longest sequence you can obtain) and go back to the BLAST website and click on pBLAST. Enter the sequence, and you will be able to verify that it is from the same organism.


You may be wondering why any of this analysis would be useful. If you take the CDS and insert it into a vector backbone (plasmid), you will be able to express a protein. Protein expression is extremely important, because a scientist can use a certain protein to develop a drug of use to humans.