Searching with BLAST
Basic Local Alignment Search Tool, or BLAST, is a tool that enables a researcher to search through large databases of sequences to find all sequences that are similar to a sequence-of-interest. Blast works by taking the researcher's sequence of interest (called the query sequence), and comparing it to every sequence in a large database of sequences. BLAST evaluates the degree of similarity and then pulls out all sequences that share at least a small region of similarity to the query. The researcher must evaluate the list of sequences to make a determination as to whether blast hits really represent true homologs. The BLAST algorithm was developed and implemented by Stephen Altschul at the U.S. National Center for Biotechnology Information
Performing a BLAST Search
Questions you must be able to answer in order to perform a blast search:
- What sequence(s) are the subject of my research? These are called query sequences. Example: I am examining the potential roles of the 10 most abundant sequences in the Chamaecrista sequence dataset. I will use these as the query sequences in a blast search.
- What subject database is the most appropriate to search, given my research question?
Example:
- If the goal is to identify potential homologs in soybean, it would be appropriate to search against the soybean genome using Phytozome.
- If the goal is to determine whether these genes have been sequenced in any other species, it would be appropriate to search against GenBank at NCBI.
- If the goal is to determine whether or not a sequence exists in the Chamaecrista transcriptome, it would be appropriate to search against the Chamaecrista transcriptome. For this search the username is Carleton and password is blastnow. If the goal is to determine whether these genes contains any functional protein domains that are known to confer particular functions, it would be appropriate to search against Pfam.
How to perform a blast search:
Step 1: Retrieve a query sequence you want to use and make sure it is in fasta format
Step 2: Navigate to the database you want to search against
Step 3: Select the BLAST programthat will use the query sequence to search the database that you selected.
Step 4: Adjust any parameters, as appropriate
