Bioinformatics and BLAST

Overview
• Recap of last time
• Similarity discussion
• Algorithms:
– Needleman-Wunsch
– Smith-Waterman
– BLAST
• Implementation issues and current
research
 Recap from Last Time
• Genome consists of entire DNA sequence
of a species
• DNA is the blueprint
• Contains individual genes
• Genes are composed of four nucleotides
(A,C,G,T)
• RNA transcribes DNA into proteins
• Proteins consist of 20 amino acids
• Proteins perform the actual functions
 Recap from Last Time
• Identify similarities among the same gene
from pig, sheep, and rabbit
• Things that were hard:
– Manually matching letters
– Deciding what “similar” meant
• Things that would have made it harder:
– What if you had the whole genome?
– What if there were missing letters/gaps?
 Why do similarity search?
• Similarity indicates conserved function
• Human and mouse genes are more than 80%
similar at sequence level
• But these genes are small fraction of genome
• Most sequences in the genome are not
recognizably similar
• Comparing sequences helps us understand
function
– Locate similar gene in another species to
understand your new gene
– Rosetta stone
 Issues to consider
• Dealing with gaps
– Do we want gaps in alignment?
– What are disadvantages of
• Many small gaps?
• Some big gaps?
 Warning: similarity not
transitive!
• If 1 is “similar” to 2, and 3 is “similar” to 2,
is 1 similar to 3?
• Not necessarily
– AAAAAABBBBBB is similar to AAAAAA and
BBBBBB
– But AAAAAA is not similar to BBBBBB
• “not transitive unless alignments are
overlapping”
 Summary
• Why are biological sequences similar to
one another?
– Start out similar, follow different paths
• Knowledge of how and why sequences
change over time can help you interpret
similarities and differences between them
 BLAST
• Basic Local Alignment Search Tool
• Algorithm for comparing a given sequence
against sequences in a database
• A match between two sequences is an
alignment
• Many BLAST databases and web services
available
 Example BLAST questions
• Which bacterial species have a protein
that is related in lineage to a protein
whose amino-acid sequence I know?
• Where does the DNA I’ve sequenced
come from?
• What other genes encode proteins that
exhibit structures similar to the one I’ve
just determined?
Background: Identifying Similarity
• Algorithms to match sequences:
– Needleman-Wunsch
– Smith Waterman
– BLAST
 Needleman-Wunsch
• Global alignment algorithm
• An example: align COELACANTH and
PELICAN
• Scoring scheme: +1 if letters match, -1 for
mismatches, -1 for gaps
COELACANTH COELACANTH
P-ELICAN-- -PELICAN--
 Needleman-Wunsch Details
• Two-dimensional matrix
• Diagonal when two letters align
• Horizontal when letters paired to gaps
C O E L A C A N T H
C O
P P
E
E E
L
L L
A
I I
C
C C
A
A A
N T H
N N - -
 Needleman-Wunsch
• In reality, each cell of matrix contains
score and pointer
• Score is derived from scoring scheme (-1
or +1 in our example)
• Pointer is an arrow that points up, left, or
diagonal
• After initializing matrix, compute the score
and arrow for each cell
 Algorithm
• For each cell, compute
– Match score: sum of preceding diagonal cell and
score of aligning the two letters (+1 if match, -1 if
no match)
– Horizontal gap score: sum of score to the left and
gap score (-1)
– Vertical gap score: sum of score above and gap
score (-1)
• Choose highest score and point arrow towards
maximum cell
• When you finish, trace arrows back from lower
right to get alignment
 Smith-Waterman
• Modification of Needleman-Wunsch
– Edges of matrix initialized to 0
– Maximum score never less than 0
– No pointer unless score greater than 0
– Trace-back starts at highest score (rather than
lower right) and ends at 0
• How do these changes affect the algorithm?
 Global vs. Local
• Global – both sequences aligned along
entire lengths
• Local – best subsequence alignment
found
• Global alignment of two genomic
sequences may not align exons
• Local alignment would only pick out
maximum scoring exon
 Complexity
• O(mn) time and memory
• This is impractical for long sequences!
• Observation: during fill phase of the
algorithm, we only use two rows at a time
• Instead of calculating whole matrix,
calculate score of maximum scoring
alignment, and restrict search along
diagonal
 Other Observations
• Most boxes have a score of 0 – wasted
computation
• Idea: make alignments where positive
scores most likely (approximation)
• BLAST
 Caveats
• Alignments play by computational, not
biological, rules
• Similarity metrics may not capture biology
• Approximation may be preferred to reduce
computational costs
• Any two sequences can be aligned
– challenge is finding the proper meaning
 BLAST
• Set of programs that search sequence
databases for statistically significant
similarities
• Complex- requires multiple steps and
many parameters
• Five traditional BLAST programs:
– BLASTN – nucleotides
– BLASTSP, BLASTX, TBLASTN, TBLASTX -
proteins
 BLAST Algorithm
• Consider a graph with one sequence
along X axis and one along Y axis
• Each pair of letters has score
• Alignment is a sequence of paired letters
(may contain gaps)
 Observations
• Recall Smith-Waterman will find maximum
scoring alignment between two sequences
• But in practice, may have several good
alignments or none
• What we really want is all statistically
significant alignments
 Observations (continued)
• Searching entire search space is
expensive!
• BLAST can explore smaller search space
• Tradeoff: faster searches but may miss
some hits
 BLAST Overview
• Three heuristic layers: seeding, extension,
and evaluation
• Seeding – identify where to start alignment
• Extension – extending alignment from
seeds
• Evaluation – Determine which alignments
are statistically significant
 Seeding
• Idea: significant alignments have words in
common
• Word is a defined number of letters
• Example: MGQLV contains 3-letter words
MGQ, GQL, QLV
• BLAST locates all common words in a pair
of sequences, then uses them as seeds for
the alignment
• Eliminates a lot of the search space
 What is a word hit?
• Simple definition: two identical words
• In practice, some good alignments may not
contain identical words
• Neighborhood – all words that have a high
similarity score to the word – at least as big
as a threshold T
• Higher values of T reduce number of hits
• Word size W also affects number of hits
• Adjusting T and W controls both speed and
sensitivity of BLAST
 Some notes on scoring
• Amino acid scoring matrices measure
similarity
• Mutations likely to produce similar amino
acids
• Basic idea: amino acids that are similar
should have higher scores
• Phenylalanine (F) frequently pairs with
other hydrophobic amino acids
(Y,W,M,V,I,L)
• Less frequently with hydrophilic amino
acids (R,K,D,E, etc.)
 Scoring Matrices
• PAM (Percent Accepted Mutation)
– Theoretical approach
– Based on assumptions of mutation probabilities
• BLOSUM (BLOcks SUbstitution Matrix)
– Empirical
– Constructed from multiply aligned protein families
– Ungapped segments (blocks) clustered based on
percent identity
Seeding Implementation Details
• BLASTN (nucleotides)– seeds always
identical, T never used
• To speed up BLASTN, increase W
• BLASTP uses W size 2 or 3
• To speed up protein searches, set W=3
and T to a large value
 Extension
• Once search space is seeded, alignments
generated by extending in both directions
from the seed
• Example:
The quick brown fox jumps over the lazy dog.
The quiet brown cat purrs when she sees him.

• Can align first six characters

• How far should we continue?
 Extension (continued)
• X parameter – How much is score allowed to
drop off after last maximum?
• Example (assume identical scores +1 and
mismatch scores -1)
The quick brown fox jump
The quiet brown cat purr
123 45654 56789 876 5654 <- score
000 00012 10000 123 4345 <-drop off
score
 What is a good value of X?
• Small X risks premature termination
• But little benefit to a very large X
• Generally better to use large value
• W and T better for controlling speed than
X
 Implementation Details
• Extension differs in BLASTN and BLASTP
• Nucleotide sequences can be stored in
compressed state (2 bits per nucleotide)
• If sequence contains N (unknown), replace
with random nucleotide
• Two-bit approximation may cause
extension to terminate prematurely
 Evaluation
• Determine which alignments are
statistically significant
• Simplest: throw out alignments below a
score threshold S
• In practice, determining a good threshold
complicated by multiple high scoring pairs
(HSPs)
 Implementation Details
• Recall three phases: seeding, extension,
evaluation
• In reality, two rounds of extension and
evaluation, gapped and ungapped
• Gapped extension and evaluation only if
ungapped alignments exceed thresholds
 Storage/Implementation
• Most BLAST databases are either a
collection of files and scripts or simple
relational schema
• What are limitations of these approaches?
 Limitations of BLAST
• Can only search for a single query (e.g. find all
genes similar to TTGGACAGGATCGA)
• What about more complex queries?
• “Find all genes in the human genome that are
expressed in the liver and have a
TTGGACAGGATCGA (allowing 1 or 2
mismatches) followed by GCCGCG within 40
symbols in a 4000 symbol stretch upstream
from the gene”
 Evaluating complex queries
• Idea: write a script that make multiple calls to
a BLAST database
• An example query plan:
1. Search for all instances of the two patterns in the
human genome
2. Combine results to find all pairs within 40
symbols of each other
3. Consult a gene database to see if pair is
upstream of any known gene
4. Consult database to check if gene expressed in
liver