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Intro To Bioinformatics Semester 6 Botany

The document discusses the aims of bioinformatics. It describes how the Needleman-Wunsch algorithm uses dynamic programming to find optimal sequence alignments but is too slow for large databases. BLAST and PSI-BLAST were developed as faster alignment tools. Another aim is predicting protein structure and interactions from sequences using computational modeling to simulate interactions like hydrogen bonding and hydrophobic effects. Bioinformatics also integrates different data types to understand organisms and disease.

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Malabika Bhowmick
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120 views

Intro To Bioinformatics Semester 6 Botany

The document discusses the aims of bioinformatics. It describes how the Needleman-Wunsch algorithm uses dynamic programming to find optimal sequence alignments but is too slow for large databases. BLAST and PSI-BLAST were developed as faster alignment tools. Another aim is predicting protein structure and interactions from sequences using computational modeling to simulate interactions like hydrogen bonding and hydrophobic effects. Bioinformatics also integrates different data types to understand organisms and disease.

Uploaded by

Malabika Bhowmick
Copyright
© © All Rights Reserved
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
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Unit 1: Introduction to Bioinformatics

Aim of Bioinformatics
Aim of Bioinformatics

The development of efficient algorithms for measuring sequence similarity is an important


goal of bioinformatics. The Needleman-Wunsch algorithm, which is based on dynamic
programming, guarantees finding the optimal alignment of pairs of sequences. This
algorithm essentially divides a large problem (the full sequence) into a series of smaller
problems (short sequence segments) and uses the solutions of the smaller problems to
construct a solution to the large problem. Similarities in sequences are scored in a matrix,
and the algorithm allows for the detection of gaps in sequence alignment.

Although the Needleman-Wunsch algorithm is effective, it is too slow for probing a large
sequence database. Therefore, much attention has been given to finding fast information-
retrieval algorithms that can deal with the vast amounts of data in the archives. An example
is the program BLAST (Basic Local Alignment Search Tool). A development of BLAST, known
as position-specific iterated- (or PSI-) BLAST, makes use of patterns of conservation in related
sequences and combines the high speed of BLAST with very high sensitivity to find related
sequences.

Another goal of bioinformatics is the extension of experimental data by predictions. A


fundamental goal of computational biology is the prediction of protein structure from an
amino acid sequence. The spontaneous folding of proteins shows that this should be
possible.
Bioinformatics is also used to predict interactions between proteins, given individual
structures of the partners. This is known as the “docking problem.” Protein-protein
complexes show good complementarity in surface shape and polarity and are stabilized
largely by weak interactions, such as burial of hydrophobic surface, hydrogen bonds, and
van der Waals forces. Computer programs simulate these interactions to predict the
optimal spatial relationship between binding partners. A particular challenge, one that
could have important therapeutic applications, is to design an antibody that binds with
high affinity to a target protein.

Initially, much bioinformatics research has had a relatively narrow focus, concentrating on
devising algorithms for analyzing particular types of data, such as gene sequences or
protein structures. Now, however, the goals of bioinformatics are integrative and are aimed
at figuring out how combinations of different types of data can be used to understand
natural phenomena, including organisms and disease.

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