2018-03-01

What is BLAST:
BLAST is a methodology to search few and short sequences against a collection of sequences (potentially millions)
The results of a BLAST search are local alignment
How does BLAST work
A database called target (subject) contains one or more sequences (could be even millions)
BLAST searches the target sequences with a query sequence
BLAST produces a list of local alignments where the query is similar to one or more target sequences.
There is another way of how does BLAST work but I cannot understand it:
Finds very short exact matches (seeds)
Extends the short exact matches to longer regions
Performs optimal alignment on the extended regions
Then applies a number of filtering on the results to reduce the results.
BLAST concepts:
Search may take place in nucleotide and/or protein space
Basic steps for using BLAST:
Prepare a BLAST database with makeblastdb. This only needs to be done once.
Pick a blast tool: blastn, blastp as appropriate (you may need to tune the parameters).
Run the tool and format the output as needed.
What are BLAST tools:
Blast is an entire suite of tools:

blast.png

Format the output differently:
Change result to output format 6 or 7 (tabular form with or without comments and headers)
Blastn –db ~refs/ebola/KM233118 –query.fa -output 7