tutorial 3 blast 1. blast tutorial how to use blast score vs. e-value exercise cool story of the...
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Tutorial 3
BLAST
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BLAST tutorial
• How to use BLAST• Score vs. E-value• Exercise
• Cool story of the day: How Alzheimer is studied in yeast
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BLAST program DatabaseQuery
BLAST
What is BLAST?• Basic Local Alignment Search Tool• Set of similarity search programs for exploring
sequence databases.
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Why perform a similarity search?
• Find genes/proteins with possibly similar function
• Find the origin of a sequence (what organism it is taken form)
• Different degrees of similarity can be found in database search
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Query type Database type
blastn Genomic Genomicblastp Proteomic Proteomicblastx Translated genomic Proteomictblastn Proteomic Translated genomic
tblastx Translated genomic Translated genomic
BLAST Databases
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Genomic: A T G CProteomic: G A S T C V L I M P F Y W D E N Q H K R
Translated genomic: The query is genomic, translated to protein using 6 possible reading frames
ATGCCGTTC -> MPF , CR, AV
Place Query
Choose Database
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Job title – helpful when running multiple runs
In case you want to restrict to a specific organism
In case you want to eliminate specific sequences
Query and DB parameters
How to choose the database?
A good place to start if you don’t know what you’re looking for
nr/nt : non-redundant nucleotide
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Depends on what you’re looking for…
Alignment parameters
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Optimizes the parameters for the
desired similarity level of the search
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Alignment parameters
Threshold for results significance
Primary word match (16-64 nt)
Scores of matching and mismatching bases
Cost to create and extend a gap
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How to interpret BLAST results?
Search for homologous to chick “olfactory receptor 6” gene
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Search results
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Query sequence
Matched sequences from DBs
Graphic Summary
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Descriptions
Sequence Identifier
+ link
Sequence description
Score(bits)
%Coverage
%Identity
E value
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Descriptions
Query covered=55%Only 55% of the query is covered => ~230 bp
Identity=71%Out of the 230 bp of alignment only 71% was of matches
E-value=But this alignment is very significant
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AlignmentsQuery info
Alignment info
Alignment
It is possible to get multiple hits
per sequence
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E-values and scores
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Score vs. E-value• The score is a measure of the similarity of the query
to the a sequence from the database. • The E-value is a measure of the reliability of the
score.
The definition of the E-value is: The number of expected alignments with observed score or higher due to chance.
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Score vs. E-value
Score (S) = (identities + mismatches) - gaps
Depends on search space
Query length(bp) Effective length (total number of bases) of the database(bp)
Depends on scoring system
Score
Bit Score (S’):
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• E-values cannot be compared across different DBs, even if the score is the same.
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Intuition for “significance”• Think of the query as a ball, each color represents a part
of the sequence.• The DB is a pool of colored balls.
• If the ball has many colors (longer query) – there is a higher probability to see the same color in the pool by chance.
• If the pool of balls is very big, there is a higher probability to see one of the balls colors in the pool.
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The typical threshold for a good E-value from a BLAST search is E=10-6≈e-6 or lower. This does not mean that higher E-values are given for queries with no biological significance.
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E-value Threshold
http://www.youtube.com/watch?v=Z7ek7UoP7Bg&src_vid=nO0wJgZRZJs&feature=iv&annotation_id=annotation_234259
E-value vs. P-valueP-value is the probability that an event will happen by chanceE-value is correction of the P-value considering the DB size.
So if the probability to find a sequence is 0.001 in a 1,000,000 entries DB the number of expected alignments we will find is 1,000!
24http://homepages.ulb.ac.be/~dgonze/TEACHING/stat_scores.pdfhttp://www.ncbi.nlm.nih.gov/BLAST/tutorial/
Exercise
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Find homologs for CFTR gene in human
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You can put the gene ID rather than
the sequence
Human DB only
We’ll start with high similarity
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Now change to more distinct
sequences
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We get more results
Find homologs for CFTR gene in other organisms
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Not only human
sequences
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Where to run a nucleotide sequence - blastn or blastx ?
blastn (genomic vs. genomics)
blastx(translated genomics vs. proteomic)
ncRNA
If you know your sequence is a protein – blastx is better, since you will get more reliable results.
Cool Story of the day
How Alzheimer is studied in yeast
Alzheimer's disease (AD)• Alzheimer's disease leads to nerve cell
death and tissue loss throughout the brain. • Symptoms can include confusion,
aggression, trouble with language, and long term memory loss. Gradually, bodily functions are lost, ultimately leading to death.
• There are no available treatments that stop or reverse the progression of the disease.
• The disease is associated with plaques and tangles in the brain.
34http://www.alz.org/braintour/alzheimers_changes.asphttp://en.wikipedia.org/wiki/Alzheimer's_disease
How can AD be studied in yeast?
Yeast cells lack the specialized processes of neuronal cells and the cell-cell communications that modulate neuropathology. However, the most fundamental features of eukaryotic cell biology evolved before the split between yeast and metazoans.
35Treusch et al. Science (2011)http://lindquistlab.wi.mit.edu/
36Thinakaran et al JOURNAL OF BIOLOGICAL CHEMISTRY 2008
Beta-amyloid () peptide is one of the hypothesized causes of AD. The most toxic form of Ab, Ab 1-42, is generated by proteolytic cleavage of APP, the transmembrane amyloid precursor protein.
Susan Linquist’s lab showed it was toxic when expressed in yeast. Later they tested the affect of this protein on rat neuron cells and in C.elegans neurons.
To recapitulate this multicompartment trafficking in yeast, we fused an endoplasmic reticulum (ER) targeting signal to the N terminus of Ab 1-42.
37Treusch et al. Science (2011)http://lindquistlab.wi.mit.edu/
• The researchers looked for suppressor genes that had homologs in Human and C.elegans
38Treusch et al. Science (2011)
Wild-type worms invariably have five glutamatergic neurons in their tails.