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BLAST and Multiple Sequence Alignment. Announcements Quiz #3 on Thurs., May 17 on lectures presented April 26, May 3 and May 15 Writing assignments due May 24 at the beginning of class. Learning objectives-Learn the basics of BLAST and Psi-BLAST and CLUSTAL W

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Blast and multiple sequence alignment
BLAST and Multiple Sequence Alignment

  • Announcements

    • Quiz #3 on Thurs., May 17 on lectures presented April 26, May 3 and May 15

    • Writing assignments due May 24 at the beginning of class.

  • Learning objectives-Learn the basics of BLAST and Psi-BLAST and CLUSTAL W

  • Workshop-Use of Psi-BLAST to determine sequence similarities.

  • Homework-Due May 20


Blast
BLAST

  • Basic Local Alignment Search Tool

  • Speed is achieved by:

    • Pre-indexing the database before the search

    • Parallel processing

  • Uses a hash table that contains neighborhood words.


Neighborhood words
Neighborhood words

  • The program declares a hit if the word taken from the query sequence has a score >= T when a scoring matrix is used.

  • This allows the word size (W) to be kept high (for speed) without sacrificing sensitivity.

  • If T is increased user the number of background hits is reduced and the program will run faster.


Which program should one use
Which Program should one use?

  • Most researchers use methods for determining local similarities:

    • Smith-Waterman (gold standard)

    • FASTA

    • BLAST

}

Do not find every possible alignment

of query with database sequence. These

are used because they run faster than S-W


What are the different blast programs
What are the different BLAST programs?

  • blastp

    • compares an amino acid query sequence against a protein sequence database

  • blastn

    • compares a nucleotide query sequence against a nucleotide sequence database

  • blastx

    • compares a nucleotide query sequence translated in all reading frames against a protein sequence database

  • tblastn

    • compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames

  • tblastx

    • compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Please note that tblastx program cannot be used with the nr database on the BLAST Web page.


Identify

Unknown

Protein

BLASTP;

General protein comparison. Use ktup=2 for speed; ktup=1 for sensitive search.

When to use a particular program

Smith-Waterman

Slower than FASTA3 and BLAST but provides maximum sensitivity

TBLASTN

Use if homolog cannot be found in protein databases; Approx. 33% slower

Psi-BLAST

Finds distantly related sequences. It replaces the query sequence with a position-specific score matrix after an initial BLASTP search. Then it uses the matrix to find distantly related sequences

Problem Program Explanation


When to use a particular program (cont. 1)

Problem Program Explanation

Identify

new

orthologs

TBLASTN:TBLASTX

Use PAM matrix <=20 or BLOSUM90 to avoid detecting distant relationships. Search EST sequences w/in the same species.

Always attempt to translate your sequence into protein prior to searching.

Identify

EST

Sequence

BLASTX;TBLASTX

Identify

DNA

Sequence

BLASTN

Nucleotide sequence comparision


Filtering repetitive sequences
Filtering Repetitive Sequences

  • Over 50% of genomic DNA is repetitive

  • This is due to:

    • retrotransposons

    • ALU region

    • microsatellites

    • centromeric sequences, telomeric sequences

    • 5’ Untranslated Region of ESTs

Example of ESTs with simple low complexity regions:

T27311

GGGTGCAGGAATTCGGCACGAGTCTCTCTCTCTCTCTCTCTCTCTCTC

TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC


Filtering repetitive sequences cont 1
Filtering Repetitive Sequences (cont. 1)

  • Programs like BLAST have the option of filtering out low complex regions. (Called Masking)

  • Repetitive sequences increase the chance of a match during a database search


Psi blast
PSI-BLAST

  • PSI-position specific iterative

  • a position specific scoring matrix (PSSM) is constructed automatically from multiple HSPs of initial BLAST search. Normal E value is used

  • The PSSM is created as the new scoring matrix for a second BLAST search. Low E value is used E=.001.

  • Result-1) obtains distantly related sequences

    2) finds the important residues that provide function or structure.


Multiple alignment
Multiple alignment

  • Learning objectives-Understand usefulness of multiple alignment. Become familiar with ClustalW algorithm. Understand the difference between ClustalW and PSI-BLAST.


Steps to multiple alignment
Steps to multiple alignment

Create Alignment

Edit the alignment to ensure that regions of functional

or structural similarity are preserved

Find conserved motifs

to deduce function

Structural

Analysis

Design of

PCR primers

Phylogenetic

Analysis


Multiple sequence alignment
Multiple Sequence Alignment

  • Collection of three or more protein (or nucleic acid) sequences partially or completely aligned.

  • Aligned residues tend to occupy corresponding positions in the 3-D structure of each aligned protein.


Practical use of msa
Practical use of MSA

  • Helps to place protein into a group of related proteins. It will provide insight into function, structure and evolution.

  • Helps to detect homologs

  • Identifies sequencing errors

  • Identifies important regulatory regions in the promoters of genes.


Clustal w thompson et al 1994
Clustal W (Thompson et al., 1994)

  • CLUSTAL=Cluster alignment

  • The underlying concept is that groups of sequences are phylogenetically related. If they can be aligned then one can construct a tree.

    • Step1-pairwise alignments

    • Step2-create a guide tree

    • Step3-progressive alignment


Flowchart of computation steps in clustal w thompson et al 1994
Flowchart of computation steps in Clustal W (Thompson et al., 1994)

Pairwise Alignment: Calculation of distance matrix

Creation of unrooted Neighbor-Joining Tree

Rooted NJ Tree (guide tree) and calculation of sequence weights

Progressive alignment following the Guide Tree


Step 1 pairwise alignments
Step 1-Pairwise alignments al., 1994)

Compare each sequence with each

other and calculate a distance matrix.

A -

B .87 -

C .59 .60 -

Different

sequences

Each number represents the number

of exact matches divided by the

sequence length (ignoring gaps).

Thus, the higher the number the more

closely related the two sequences are.

A B C

In this distance matrix, sequence A is 87% identical to sequence B


Step 1 pairwise alignments1
Step 1-Pairwise alignments al., 1994)

Compare each sequence with each

other and pairwise alignment scores

human EYSGSSEKIDLLASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTEN 480

Dog EYSGSSEKIDLMASDPQDAFICESERVHTKPVGGNIEDKIFGKTYRRKASLPKVSHTTEV 477

mouse GGFSSSRKTDLVTPDPHHTLMCKSGRDFSKPVEDNISDKIFGKSYQRKGSRPHLNHVTE 476

  • SeqA Name Len(aa) SeqB Name Len(aa) Score

  • human 60 2 dog 60 76

  • 1 human 60 3 mouse 59 57

  • 2 dog 60 3 mouse 59 49


Step 2 create guide tree

human:0.07429 al., 1994)

dog:0.15904

mouse:0.3494

Guide Tree

Sreal(ij) – Srand(ij)

Sident(ij) – Srand(ij)

Seff =

x 100

Step 2-Create Guide Tree

Use the Distance Matrix to create a Guide Tree to

determine the “order” of the sequences.

Distance from random sequence

H -

D 76 -

M 57 49 -

Different

sequences

H D M

Branch length proportional

to estimated divergence

between dog and other sequences

D = -ln(Seff)

( human:0.07429, dog:0.15904, mouse:0.34944);


Step 3 progressive alignment

human:0.07429 al., 1994)

dog:0.15904

mouse:0.3494

Guide Tree

Step 3-Progressive Alignment

Align human and dog first. Then add mouse to the

previous alignment. In the closely aligned sequences

gaps are given a heavier weight (positive value) than gaps in more diver-

gent sequences. “once a gap always a gap”

Why a heavier weight for the closely aligned sequences?

Because those gaps suggest separations between functional or

structural entities. In more divergent sequences

gaps may be produced as an artifact of sequences

that are dissimilar.


Gap treatment
Gap treatment al., 1994)

  • Short stretches of 5 hydrophilic residues often indicate loop or random coil regions (not essential for structure) and therefore gap penalties are reduced reduced for such stretches.

  • Gap penalties for closely related sequences are lowered compared to more distantly related sequences (“once a gap always a gap” rule). It is thought that those gaps occur in regions that do not disrupt the structure or function.

  • Alignments of proteins of known structure show that proteins gaps do not occur more frequently than every eight residues. Therefore penalties for gaps increase when required at 8 residues or less for alignment. This gives a lower alignment score in that region.

  • A gap weight is assigned after each aa according the frequency that such a gap naturally occurs after that aa in nature


Amino acid weight matrices
Amino acid weight matrices al., 1994)

  • As we know, there are many scoring matrices that one can use depending on the relatedness of the aligned proteins.

  • As the alignment proceeds to longer branches the aa scoring matrices are changed to accommodate more divergent sequences. The length of the branch is used to determine which matrix to use and contributes to the alignment score.


Flowchart of computation steps in clustal w thompson et al 19941
Flowchart of computation steps in Clustal W (Thompson et al., 1994)

Pairwise Alignment: Calculation of distance matrix

Creation of unrooted Neighbor-Joining Tree

Rooted NJ Tree (guide tree) and calculation of sequence weights

Progressive alignment following the Guide Tree



Example of sequence alignment using clustal w
Example of Sequence Alignment using Clustal W al., 1994)

Asterisk represents identity

: represents high similarity

. represents low similarity


Multiple alignment considerations
Multiple Alignment Considerations al., 1994)

  • Quality of guide tree. It would be good to have a set of closely related sequences in the alignment to set the pattern for more divergent sequences.

  • If the initial alignments have a problem, the problem is magnified in subsequent steps.

  • CLUSTAL W is best when aligning sequences that are related to each other over their entire lengths

  • Do not use when there are variable N- and C- terminal regions

  • If protein is enriched for G,P,S,N,Q,E,K,R then these residues should be removed from gap penalty list. (what types of residues are these?)

Reference: http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/


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