BLAST Flashcards
What are the major types of BLAST searches?
BLASTn, BLASTx, BLASTp
What does a BLASTn search do?
nucleotide query to nucleotide database Mainly useful for very closely related species
What does a BLASTx search do?
nucleotide query to protein database
What does a BLASTp search do?
protein query to protein database
What does a BLAST search do?
Provides a method for rapid similarity searching of nucleotide and protein databases
What does the E-value: expectation value represent in BLAST?
“The number of hits one can expect to find by chance (the background noise) when searching a database of a particular size”
- represents the significance of each hit
ID intron, first exons, 5’UTR, and 3’UTR on
compliment(join(<428…533, 1288…1475))
/gene = “BCRA2”
2 exons: position 1475-1288 and 533-428 on the reverse strand
1 intron is located from position 1287-534.
5’UTR is upstream of position 1475
3’UTR is downstream from position <428
How much of the query sequence is alignable to the subject sequence?
Look for the query cover (%)
- a number that describes HOW MUCH of the query sequence is covered by the target sequence.
Evaluate insertions/deletions in BLAST results
Indicated by a GAP
- introduced into an alignment to compensate for insertions and deletions in one sequence relative to another.
What is the percent identity between two sequences?
The percent identity is a number that describes HOW SIMILAR the query sequence is to the target sequence (how many characters in each sequence are identical).
Interpret the E-Values?
The lower the E value is, the more significant the match.
Interpret percent identity?
The higher the percent identity is, the more significant the match.
Interpret query coverage?
If the target sequence in the database spans the whole query sequence, then the query cover is 100%. This tells us how long the sequences are, relative to each other.
