BLAST (Basic Local Alignment Search Tool) is a set of algorithms available at NCBI that allow you to use a DNA, RNA or protein sequence to find similar sequences in the NCBI databases. There are many flavors of BLAST that accomodate different types of sequence, but they operate in similar ways. See below for more details
An E-value, aka the “expect value”, is the number of matches you’d expect to get by random chance in a given database/query combo (false positives). Smaller numbers are better because false positives are bad. This depends on the length of the query and the size of the database.
For example, if you search two databases with the same sequence, you would get different expect values depending on the size of the databases. The E-value would be bigger in the larger databases, because it provides more opportunity for false positives.
An alignment score is a measure of how well the query and a given search result (subject) are aligned.
The score is determined by the scoring parameters like match/mismatch scores, which are usually positive for matching bases and negatives for mismatched bases, and gap penalties, which have negative scores for opening and extending gaps in the alignment.
Higher alignment scores are better, but they depend heavily on sequence length, so don't try to compare alignment scores between different BLAST queries.
Before you can use BLAST, here's the information you need:
Your advisor walks in to the lab and says:
"I have this nucleotide sequence derived from wild-type mouse DNA. What gene is it? What does this gene do?"
How do you figure this out? USE BLAST!
Entering your query: