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Clemson bioinformatics sequence alignments

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Section 1

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PSI-BLAST

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Last updated

6 years ago

Date created

Mar 1, 2020

Cards (17)

Section 1

(17 cards)

PSI-BLAST

Front

constructs a position-specific scoring matrix (PSSM) and is well suited for identification of distantly related proteins

Back

dotplot

Front

simple picture that gives an overview of the similarities between two sequences

Back

E value

Front

is an estimate of the number of false positives from a BLAST search from a random sequence

Back

BLAST

Front

a local alignment that searches databases using query words

Back

Position-specific Iteration BLAST (PSI-BLAST) is particularly well suited for identification of distantly related proteins though constructing a position-specific scoring matrix (PSSM) to facilitate the search

Front

True

Back

TBLASTN

Front

searches a protein query against a translated nucleotide sequence database

Back

If you have 2 distantly related protein sequences to align and compare, which BLOSUM or PAM matrix would be more appropriate?

Front

low BLOSUM high PAM

Back

BLASTP

Front

searches protein query against a protein sequence database

Back

what does a shift in a diagonal line on a dot plot mean?

Front

insertion

Back

T/F: BLAST is a rapid, heuristic version of the smith-waterman algorith,, and BLAST starts database searching with query words

Front

True

Back

sequence alignment

Front

the identification of residue-residue correspondence

Back

BLOSUM

Front

BLOcks SUbstitution Matrix. this is a database

Back

PAM

Front

Point Accepted Mutation. measures mutation rate

Back

BLASTX

Front

searches a translated nucleotide query against a protein sequence database

Back

BLASTN

Front

searches nucleotide query against nucleotide sequence database

Back

which provides the best estimate of the false positives from a BLAST search?

Front

e value

Back

how to handle too many results

Front

§Select a RefSeq database to reduce redundancy §Limit the results by an organism or group §Adjust the scoring matrix §Use just a portion of the query sequence

Back