Heuristic approaches scoring matrices
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HEURISTIC APPROACHES

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Heuristic approaches scoring matrices

Heuristic approaches & scoring matrices

M.Prasad Naidu

MSc Medical Biochemistry, Ph.D,.


Introduction

Introduction

  • Two algorithms are there in these methods

    • BLAST

    • FASTA

  • FastA is an algorithm developed by Pearson and Lipman. Its more sensitive than Blast.

  • Blast is an algorithm developed by Altschul et al., in 1990. It provides tools for high scoring local alignment between two sequences. Now a days, a gapped versions are available.


Blastp algorithm

BLASTP algorithm

  • Blast Algorithm involves the following steps.

    • Breaking of the sequence into defined word size.

    • Finding a match or HSP (High Scoring Pair).

    • Alignment of the word and extending the alignment.


Breaking of the sequence into defined word size

Breaking of the sequence into defined word size

Query : AILDTGATGDA

Word size : 4

AILDTGATGDA

AILD

ILDT

LDTG

DTGA

TGAT

GATG

ATGD

TGDA


Finding a high scoring pair

Finding a High scoring Pair

MQVWGWAILDTVATDAAMLL

AILD


Extending the alignment

Extending the alignment

MQVWGWAILDTVATDAAMLL

……………..AILDTGATGDA……

Parameters in BLAST result

Percentage of Homology

Scoring of the alignment

No of residues aligned

E-value


Fasta algorithm

FastA algorithm

  • The word size in FastA algorithm is defined as K-tuple.

  • Generally the K-tuple for the algorithm is either 3 or 4 for nucleotide sequences and 1 or 2 for protein sequences.

  • FastA algorithm also involves the steps similar to that of the BLAST tool. But the alignment generation procedure is different.


Breaking of the sequence into defined k tuple

Breaking of the sequence into defined k-tuple

F A M L G F I K Y L P G C M

1 2 3 4 5 6 7 8 9 10 11 12 13 14


Heuristic approaches

The most occuring number in the algorithm is 3, so the alignment starts after leaving three characters or residues


Alignment of the sequences

Alignment of the sequences

F A M L G F I K Y L P G C M

T G F I K Y L P G A C T

Parameters in FASTA result

Percentage of Homology

Scoring of the alignment

No of residues aligned

P-Score


Scoring schemes

Scoring schemes

Identity scoring matrix

  • Residue to residue scores are represented here in the form of similarity.

  • A 4 X 4 matrix is built for the nucleotides and 20 X 20 matrix for the amino acids.

  • For match score is +1 and mismatch is -1


Pam matrices

PAM Matrices

  • These were first developed by Margaret Dayhoff and co-workers in 1978.

  • This model assumes that evolutionary changes follow the markov model i.e. residual changes occur independent on the previous mutation. One PAM is a unit of evolutionary divergence in which there is 1% amino acid change but it doesn’t imply that 100 PAM results in different aminoacids.

  • Dayhoff and coworkers have calculated the frequencies of accepted mutations for 1PAM by analyzing closely related families of sequences.

  • The scores are represented as log odd ratios.

  • The 1PAM can be extended to any no of PAMS. For example, 1PAM table is extended to N X 1PAM.

  • For closely related protein sequences, lower distance PAM is used and higher PAM is used for variying proteins.

  • PAM 30 is used for closer proteins and PAM 250 for divergent ones.


Pam 250 scoring matrix

PAM 250 scoring matrix


Blosum matrices

BLOSUM Matrices

  • These matrices are developed by Heinkoff and Heinkoff in 1991.

  • The matrices have been constructed in a similar fashion as PAM matrices.

  • The data was derived for local alignment of distantly related proteins deposited in the BLOCKS database.

  • BLOSUM 30 is used for comparing highly divergent sequences and BLOSUM 90 is used for closely related proteins.

  • Commonly used BLOSUM matrix is BLOSUM 62 that is used for proteins with 62% identities.


Blosum 62 matrix

BLOSUM 62 Matrix


Thank you

THANK YOU


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