BLAST

You have a reasonably short, typical, double-stranded DNA sequence. Basically, how many proteins can it potentially encode?

• 1

• 2

• 3

• 6

You have a DNA sequence. You want to know which protein in the main protein database ("nr,", the nonredundant database) is most similar to some protein encoded by your DNA. Which program should you use?

• BLASTN
• BLASTP
• BLASTX
• TBLASTN
• TBLASTX

Which output from a BLAST search provides an estimate of the number of false positives from a BLAST search?

• E value

• bit score

• percent identity

• percent positives

• query cover

Changing which of the following BLAST parameters would tend to yield fewer search results?

• turning off the low-complexity filter
• changing the expect value from 1 to 10
• raising the threshold value
• changing the scoring matrix from PAM30 to PAM70

You can limit a BLAST search using any ENTREZ term. For example, you can limit the results to those containting a researcher's name.

• TRUE

• FALSE

An extreme value distribution:

• describes the distribution of scores from a query against a database
• has a larger total area than a normal distribution
• is symmetric
• has a shape that is described by two constants; the mean and the decay constant

As the E value of a BLAST search becomes smaller

• the value K also becomes smaller
• the score tends to be larger
• the probability p tends to be larger
• the extreme value distribution becomes less skewed

The BLAST algorithm compiles a list of "words" typically of three amino acids (for a protein search). Words at or above a threshold value T are defined as:

• "hits," and are used to scan a database for exact matches that may then be extended

• "hits," and are used to scan a database for exact or partial matches that may then be extended

• "hits," and are aligned to each other

• "hits," and are reported as raw scores

Normalized BLAST scores (also called bit scores):

• are unitless
• are not related to the scoring matrix that is used
• can be compared between different BLAST searches, even if different scoring matrices are used
• can be compared between different BLAST searches, but only if the same scoring matrices are used

BLASTP is used to search a

• Nucleotide query against a nucleotide sequence database

• Protein query against a translated nucleotide sequence database

• Translated nucleotide query against a protein database

• Protein query against a protein database

• Translated nucleotide query against a translated nucleotide database