LSM2241 Practical 4

Part 1
Introduction to BLAST
BLAST Programs
BLAST
Program
Translation
of Query
Query
Type
Translation
of Subject
Subject
Type
Resulting
Comparison
blastn No Nucleotide No Nucleotide
Nucleotide vs.
Nucleotide
blastp No Protein No Protein
Protein vs.
Protein
blastx Yes Nucleotide No Protein
Protein vs.
Protein
tblastn No Protein Yes Nucleotide
Protein vs.
Protein
tblastx Yes Nucleotide Yes Nucleotide
Protein vs.
Protein
Databases for BLAST
Nucleotide databases
GenBank
NCBI Nucleotide database
Nucleotide collection (nt)
Refseq_Genomic
Refseq_RNA
Databases for BLAST
Protein databases
GenPept
NCBI Protein database
Non-redundant protein sequences (nr)
RefSeq_Protein
SwissProt
BLAST SEARCH
LSM2241 Practical 4 Part 1
BLAST Search
Sequence similarity
Infer homology
If two sequences are significantly similar over their
entire length, they are likely to be homologous
Homology cannot be measured
Parameters for blastn
Expected number of
chance matches in a
random model. If
statistical significance
ascribed to the match
is greater than the
threshold, it will not
be reported
Length of window that
initiates an alignment
Reward and penalty for
matching and
mismatching bases
Cost to create and
extend a gap.
Restrictions on affine
penalties.
Sequences with low
compositional complexity such
as repeats
Filter On
Removes regions of low
complexity, which can be
misleading
Filter Off
High scoring but biologically
uninteresting hits may be
generated
Parameters for blastp, blastx and
tblastn
Default: 3 amino acids
Changes depending
on type of sequence
you are searching
Only the affine gap
penalty model is
considered
Adjustment of scoring
matrix to compensate
for amino acid content
of the sequences being
compared
Parameters for tblastx
Only un-gapped
alignments are
considered
Key Parameters for Analysis
Length of the alignment
Alignment score in
format normal bits (raw)
Expect Reliability of Score
Percentage identity of
query sequence vs.
subject sequence
No. of identical residues
No. of identical residues
and similar residues
Lets BLAST!
Task 1
What is a frame?
When does it appear in the alignment results?
When does it not appear in the alignment results?
Quick Quiz
Identify the BLAST program that generated
the given output