BASICS OF BIOINFORMATICSBiotechnology Division

North-East Institute of Science & Technology(Council of Scientific & Industrial Research)

Jorhat 785 006, Assam

Salam PradeepEmail: salampradeep@gmail.com

Bioinformatics• Use of techniques including • Applied mathematics• Informatics• Statistics• Computer science• Artificial intelligence,• Chemistry & Biochemistry• To solve biological problems on the molecular

level

Major Research Efforts & Applications

Sequence analysis & alignment• Comparison of sequence in order to find the

similar sequence. • Way of arranging the sequences of DNA / RNA

/ Amino Acids to identify regions of similarity that may be a consequence of functional, structural or evolutionary relationships.

• Identification of gene structures, reading frames, distributions of introns & exons & regulatory elements.

Genome annotation• Process of marking the genes and other biological

features in a DNA sequence• First genome annotation software system was

designed in 1995 by Dr. Owen White• First genome of a free-living organism to be

decoded, the bacterium Haemophilus influenzae.• White’s software system finds the genes (places

in the DNA sequence that encode a protein), the transfer RNA, and other features.

Computational evolutionary biology• Trace the evolution of a large number of

organisms by measuring changes in their DNA, rather than through physical taxonomy or physiological observations alone.

• Compare entire genomes, permits the study of more complex evolutionary events, such as gene duplication, horizontal gene transfer, speciation.

• Track and share information on an increasingly large number of species and organisms

Measuring biodiversity• Biodiversity Databases are used to collect the

species names, descriptions, distributions, genetic information, status & size of populations, habitat needs, and how each organism interacts with other species.

• Computer simulations model such things as population dynamics, or calculate the cumulative genetic health of a breeding pool (in agriculture) or endangered population (in conservation).

• Entire DNA sequences, or genomes of endangered species can be preserved, allowing the results of Nature's genetic experiment to be remembered in silico, and possibly reused in the future, even if that species is eventually lost.

Prediction of protein structure• Protein structure prediction is one of the most

important goals pursued by bioinformatics and theoretical chemistry.

• Its aim is the prediction of the three-dimensional structure of proteins from their amino acid sequences.

• In other words, it deals with the prediction of a protein's tertiary structure from its primary structure.

• Protein structure prediction is of high importance in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes).

Comparative genomics• Comparative genomics is the study of the

relationship of genome structure and function across different biological species or strains.

• Gene finding is an important application of comparative genomics, as is discovery of new, non-coding functional elements of the genome.

• Computational approaches to genome comparison have recently become a common research topic in computer science.

Modeling biological systems

• Systems biology involves the use of computer simulations of cellular subsystems such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks) to both analyze and visualize the complex connections of these cellular processes.

• Artificial life or virtual evolution attempts to understand evolutionary processes via the computer simulation of simple (artificial) life forms.

Protein-protein interaction & docking

• Protein-protein interactions involve the association of protein molecules.

• These associations are studied from the perspective of biochemistry, signal transduction and networks.

• Wet Lab Techniques: Co-immunoprecipitation, FRET, Bimolecular Fluorescence Complementation

• Protein-protein docking: the prediction of protein-protein interaction based on the three-dimensional protein structures only is not satisfactory As of 2006.

Biological Sequence Database

Primary Sequence Databases

• The International Nucleotide Sequence Database (INSD) consists of the following databases.

• DDBJ (DNA Data Bank of Japan) • EMBL Nucleotide DB (European Molecular

Biology Laboratory) • GenBank (National Center for Biotechnology

Information) • They interchange the stored information and

are the source for many other databases

NCBI• National Center for Biotechnology Information is

part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health.

• Founded in 1988 sponsored by Senator Claude Pepper.

• NCBI has had responsibility for making available the GenBank DNA sequence database since 1992

• In addition to GenBank, NCBI provides OMIM, MMDB (3D protein structures), dbSNP, the Unique Human Gene Sequence Collection, a Gene Map of the Human genome, a Taxonomy Browser etc

DDBJ

EMBL

Protein Sequence Database

UniProt - Universal Protein Resource

Swiss-Prot - Protein Knowledgebase

Protein Information Resource

Pfam

Protein Structure Databases

Protein Data Bank (PDB)

PDB Statistics

NCBI Molecular Modeling Database

Genome Databases

Corn

ERIC (Enteropathogen Resource Integration Center)

Flybase

MGI Mouse Genome

Viral Bioinformatics Resource Center

Saccharomyces Genome Database

National Microbial Pathogen Data Resource

Other Databases• Protein-protein interactions - BioGrid, STRING, DIP etc• Metabolic pathway Databases - KEGG, BioCyc, MANET etc• Microarray databases - ArrayExpress, Stanford Microarray Dbase, GEO

Sequence File Formats• FASTA – Always starts with a > (greater than

symbol) • GENBANK – Series of header lines - Locus, Definition, Origin …• EMBL – 1st line begins the first sequence entry - 1st line of entry contains 2 letter ID

FASTA Format

GenBank Format

EMBL Format

Inside NCBI

Sitemap

Taxonomy Browser

NCBI Taxonomy Browser Statistics

Genome Projects

Genome Projects Statistics

Map Viewer

Sequence analysis &

Sequence alignment

Sequence analysis & alignment• Comparison of sequences in order to find

similar sequences • A way of arranging the sequences of

DNA/RNA/PTN to identify regions of similarity that may be a consequence of functional, structural or evolutionary relationships.

• Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix

Representations in Sequence alignment

Semi Conservative Substitution

Conservative Substitution

Global and Local alignments • Global alignments attempt to align every

residue in every sequence• Most useful when the sequences in the query

set are similar and of roughly equal size. • Local alignments are useful for dissimilar

sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context.

• With sufficiently similar sequences - there is no difference between local and global alignments.

• Needleman-Wunsch algorithm - A general global alignment technique and is based on dynamic programming

• Smith-Waterman algorithm - A general local alignment method also based on dynamic programming.

Pairwise alignment • Used to find the best-matching piecewise local

or global alignments of two query sequences. • It can only be used between 2 sequences at a

time• Efficient to calculate and are often used for

methods such as searching a database for sequences with high homology to a query.

• Primary methods of producing pairwise alignments are dot-matrix methods, dynamic programming, and word methods

Multiple sequence alignment • MSA incorporate more than two sequences at

a time • Multiple alignment align all of the sequences

in a given query set • Often used in identifying conserved sequence

regions across a group of sequences• Aid in establishing evolutionary relationships

by constructing phylogenetic trees

Sequence Similarity Search

NCBI BLAST• An algorithm for comparing primary biological

sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences

• A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold.

• BLAST program was designed by Eugene Myers, Stephen Altschul, Warren Gish, David J. Lipman and Webb Miller at the NIH and was published in J. Mol. Biol. in 1990

BLAST Types• blastn - Nucleotide-nucleotide BLAST • blastp - Protein-protein BLAST • blastx - Nucleotide 6-frame translation-

protein• tblastx - -Nucleotide 6-frame translation-

nucleotide 6-frame translation • tblastn - Protein-nucleotide 6-frame

translation• megablast - Large numbers of query

sequences

BLASTn

BLASTp

BLASTn: Search Set

BLASTp: Search Set

BLASTn: Program Selection

BLASTp: Program Selection

BLASTn Result

BLASTn: Graphic Summary

BLASTn Description

BLASTn Alignment

BLASTn Tree View

PDB BLASTp

BLASTp: Graphic Summary

PDB BLASTp Description

PDB BLASTp Alignment

BLASTp Tree View

Multiple Sequence Alignment

EBI ClustalW Server

Preparing Multiple Sequence

Phylogenetic Analysis

Cladogram• A Cladogram is a branching diagram (tree) assumed to be

an estimate of a phylogeny where the branches are of equal length, thus cladograms show common ancestry, but do not indicate the amount of evolutionary "time" separating taxa.

Phylogram• Phylogram is a branching diagram (tree) assumed to be

an estimate of a phylogeny, branch lengths are proportional to the amount of inferred evolutionary change.

JalView – Java Applet

Thank You