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Blast 2 Sequences: Salman Khan Current Gpa in Bioinf 4 Gpa

This document describes the BLAST 2 SEQUENCES tool, which allows users to compare two protein or nucleotide sequences. BLAST 2 SEQUENCES finds multiple local alignments between the two input sequences using heuristic algorithms like dynamic programming and Smith-Waterman. Users can adjust parameters like the scoring matrix and gap penalties to refine the alignments. The output includes a graphical representation of the alignments found and BLAST-style statistics. BLAST 2 SEQUENCES extends the capabilities of traditional BLAST by allowing gapped alignments between query and subject sequences.

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75 views45 pages

Blast 2 Sequences: Salman Khan Current Gpa in Bioinf 4 Gpa

This document describes the BLAST 2 SEQUENCES tool, which allows users to compare two protein or nucleotide sequences. BLAST 2 SEQUENCES finds multiple local alignments between the two input sequences using heuristic algorithms like dynamic programming and Smith-Waterman. Users can adjust parameters like the scoring matrix and gap penalties to refine the alignments. The output includes a graphical representation of the alignments found and BLAST-style statistics. BLAST 2 SEQUENCES extends the capabilities of traditional BLAST by allowing gapped alignments between query and subject sequences.

Uploaded by

Xâlmañ Kháñ
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PPTX, PDF, TXT or read online on Scribd
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BLAST 2

SEQUENCES

SALMAN KHAN

CURRENT GPA IN BIOINF 4 GPA


BLAST 2 SEQUENCES

A new tool for comparing protein and nucleotide sequences


Group members
Head of the team
Salman Khan (046)
Memebers
– Ahmer Shoaib (002)
– Ammar Baig (024)
– Humayun Asghar (037)
– Malik Hamza (113)
– Muhammad Kashif (043)
Background

What is sequence Alignment?


Purpose of Sequence Alignment?
Types of Sequence alignment:
Software use for Sequence alignment:
What is Blast:
Needleman–Wunsch algorithm
Smith–Waterman algorithm
Presented by

Mr. Salman Khan


(FA17-BCS-046/ATK)
What is sequence
Alignment?

In bioinformatics, a sequence alignment is a


way of arranging the sequences of DNA,
RNA, or protein to identify regions of
similarity that may be a consequence of
functional, structural, or evolutionary
relationships between the sequences.
Purpose of Sequence
Alignment?

The purpose of sequence alignment was to find the highly


similarity region from your query sequence.
Types of Sequence
alignment:

There are two types of sequence alignment


– Local alignment
– Global alignment
Local alignment and Global
Alignment

In a local alignment, you try to match your query with a


substring (a portion) of your subject
In a global alignment, you perform an end to end alignment
with the subject
Software use for Sequence
alignment:

– LALIGN-pairwise alignment
– Clustal-W - the famous Clustal-W multiple alignment program

– GOR – protein secondary structure prediction


Blast (Basic Local Alignment Search
Tool)

BLAST finds regions of similarity between biological


sequences. The program compares nucleotide or protein
sequences to sequence databases and calculates the
statistical significance.
Sequences Entered

Two type of sequences can be entered in blast


– Nucleotide BLAST

– Protein BLAST
Continue…….

BLAST compares protein and nucleotide sequences much


faster than dynamic programming methods such as Smith-
Waterman and Needleman-Wunsch .
Needleman–Wunsch
algorithm

– The Needleman–Wunsch algorithm is an algorithm used


in bioinformatics to align protein or nucleotide sequences.
– It divides large problems into
subproblems.
– It is also sometimes referred to
as the optimal matching
algorithm and the
global alignment technique.
Needleman–Wunsch
algorithm

Steps:
1.Constructing the grid.
2.Choosing a scoring system.
3.Filling the table.
4.Tracing arrows back to origin.
5.Find optimal alignment .
Smith-Waterman

The Smith–Waterman algorithm performs local sequence


alignment; that is, for determining similar regions between
two strings of nucleic acid sequences or protein sequences.
Smith-Waterman

Steps:
1. Determine the substitution matrix and the gap penalty
scheme.
2. Initialize the scoring matrix.
3.Scoring.
4. Trace back.
Differences
Smith–Waterman Needleman–Wunsch
algorithm algorithm

First row and first column First row and first column
Initialization
are set to 0 are subject to gap penalty

Scoring Negative score is set to 0 Score can be negative

Begin with the highest Begin with the cell at the


Traceback score, end when 0 is lower right of the matrix,
encountered end at top left cell
Next Humayun explain the topic
of blast 2
BLAST2

BLAST 2 SEQUENCES’, a new BLAST‐based tool for aligning two


protein or nucleotide sequences, is described.
The BLAST 2 SEQUENCES program finds multiple local
alignments between two sequences, allowing the user to
detect homologous protein domains or internal sequence
duplications.
Blast2 Input
Blast2 Output
Blast2 Output
Now Ahmer will explain the
algorithm
Algorithm

The algorithm of Blast2 was


based on
Dynamic approach
Heuristic method
Dynamic programming

Dynamic programming (also known as dynamic


optimization) is a method for solving a complex problem by
breaking it down into a collection of simpler sub problems,
solving each of those sub problems just once, and storing
their solutions.
Heuristic method:

In heuristic method we made an educated guess


Now Kashif will explain the
more about algorithm
USER DEFINED PARAMETERS

– The `BLAST 2 SEQUENCES' interface allows the user to


perform a series of searches with various parameters.

– Different scoring matrices are provided for protein-protein


comparisons
SCORING MATRIX
Scoring Matrix :
Scoring matrices are used to determine the
relative score made by matching two characters in a sequence
alignment.
TYPES:

1.PAM (POINT ACCEPTED MUTATION)


2.BLOSSUM (BLOCK SUBSTITUTION MATRIX)
PAM (POINT ACCEPTED
MUTATION)

– IT IS USED FOR SCORE ALIGNMENT BETWEEN CLOSELY


RELATED PROTIEN
– BASED ON GLOBAL ALIGNMENT
– ALIGNMENTS HAVE HIGH SIMILARITY THEN BLOSUM
ALIGNMENT
BLOSUM(BLOCK
SUBSTITUION MATRIX)

– USED TO FIND SCORE ALIGNMENT BETWEEN


EVOLUTIONARY DIVERGENT PROTIEN SEQUENCE
– BASED ON LOCAL ALIGNMENT
– ALIGNMENTS HAVE LOW SIMILARITY THEN PAM
ALIGNMENT
CONT…

Each matrix is most sensitive at finding similarities.

The default matrix, BLOSUM62 is generally considered to be


the
best for a wide variety of distances
CHANGES

– By changing the GAP existence penalties the number and


length of
gaps in an alignment can be changed

– Each scoring Matrix has its default value for the GAP
Penalty .
ERROR

An incorrect parameter setting returns an error response


and brings back the main page, allowing the user to change
the selection.
Now Ammar will explain about
the results and findings
RESULT AND DISCUSSION
RESULT AND DISCUSSION

– The result starts with the values of parameters that were


selected to produce the results.
– The user can recalculate the alignments by changing the
parameters
– Clicking on the `Align' button, which provides a fast and
convenient way of comparing the results for different
values of parameters.
RESULT AND
DISCUSSION

– The graphical representation shows schematically the set


of gapped local alignments found between the two
sequences with gaps shown in red.
– Clicking on the graphics brings the user to the detailed
representation of that alignment described below.
RESULT AND
DISCUSSION
– The last part of the report shows the parameter of calculations and the
summary of BLAST statistics. The report is the same as the regular BLAST
report, providing an easy way to compare the results of alignment of two
sequences with the result of an entire database search.
Now Malik Hamza Explain
about Conclusion and References
Conclusion

– (Original BLAST) Only ungapped alignments sometimes


combined together.
– (BLAST2) Extend the HSPs using gapped alignment
References

– [1] Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and
Lipman, D.J. (1990) Basic local alignment search tool. J.
Mol. Biol. 215, 403-410.
– [2] Altschul, S.F., Madden, T.L., A.A., Zhang, J., Zhang, Z.,
Miller, W. and Lipman, D.J. Res. 25, 3389-3402.
References

– [3] Smith, T.F. and Waterman, M.S. (1981) Identification of


common molecular subsequences. J. Mol. Biol. 147,
195^197.
– [4] Needleman, S.B. and Wunsch, C.D. (1970) A general
method applicable to the search for similarities in the
amino acid sequences of two proteins. J. Mol. Biol. 48, 443-
453.
References

– [5] Tomb, J.-F., White, O., Kerlavage, A.R., Clayton, R.A.,


Sutton, G.G., Fleischmann, R.D., Ketchum, K.A., Klenk, H.P.,
Gill, S., Dougherty, B.A., Nelson, K., Quackenbush, J., Zhou,
L., Kirkness, E.F., Peterson, S., Loftus, B., Richardson, D.,
Dodson, R., Khalak, H.G., Glodek, A., McKenney.
– [6] Alm, R.A., Ling, L.-S.L., Moir, D.T., King, B.L., Brown, E.D.,
Doig, P.C., Smith, D.R., Noonan, B., Guild, B.C., deJonge,
B.L., Carmel, G., Tummino, P.J., Caruso, A., UriaNickelsen,
M., Mills, D.M., Ives, C., Gibson, R.

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