BLAST searching with short sequences
There are a number of reasons why you might want to search with short sequences:
- you have a short functional piece of DNA or protein, and you wish to find other sequences that contain it
- you have carried out a proteomics experiment (more on that below) and have sequenced some short peptides and now wish to find the proteins that produced them
- you wish to PCR something in the lab, and you need to check the primers are not in other DNA sequences
Proteomics is the study of all the proteins expressed in a cell at a given time. When a cell becomes diseased or stressed it will change its protein profile and express different proteins. Also, some disease states are caused by the expression of proteins, or by mutated proteins, and these need to be identified.
In a typical proteomics experiment, you take cells from a 'healthy state' (control) and compare their protein profile to cells that are in the 'diseased' state. This is usually done by a gel or column chromatography, so 'differences' can be isolated (purified). The purified proteins are then identified by mass-spectrometry, which returns short peptide sequences.
All you need to know for the next section is that you have some short peptide sequences, and you need to identify the protein that produced them.
In PCR you use short sequences of DNA (typically 18 - 25 bases) called primers to amplify DNA. Besides checking the primers for melting temperature, the formation of hair-pin loops and primer-dimer pairs, you might also want to check that the primers do not match any other DNA sequences as they may also amplify those.
In this section, we will also look at searching with short sequences of DNA (primers).