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 typeblastn 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

http://blast.ncbi.nlm.nih.gov/Blast.cgi 6

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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Optimize 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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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 this 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.

‘

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!

23http://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.

33http://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.

34Treusch et al. Science (2011)http://lindquistlab.wi.mit.edu/

• Beta-amyloid () peptide is one of the hypothesized causes of AD.

• 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.

35Treusch et al. Science (2011)http://lindquistlab.wi.mit.edu/

• The researchers looked for suppressor genes that had homologs in Human and C.elegans

36Treusch et al. Science (2011)