1 Bio + Informatics AAACTGCTGACCGGTAACTGAGGCCTGCCTGCAATTGCTTAACTTGGC An Overview پرتال پرتال بيوانفورماتيك ايرانيان.

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Bio + InformaticsAAACTGCTGACCGGTAACTGAGGCCTGCCTGCAATTGCTTAACTTGGC

An Overview

WWW.IBP.IR بيوانفورماتيك پرتالايرانيان

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Outline

• Introduction• DNA• Definitions• Problems in bioinformatics• Conclusion

AAACTGCTGACCGGTAACTGAGGCCTGCCTGCAATTGCTTAACTTGGC

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Sciences reach a point where they become

mathematized!“Leonard Adleman”

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Computing Devices

• Computers→ electronic components (transistors,…)

• Brains→ biological components (neurons, …)

• Cells→ biomolecular components (DNA,…)


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DNA

• Deoxyribonucleic acid: DNA• Four nucleotides (bases), or building blocks:

A, T, G, C• Zips itself up into helixes using base pairs:

→ A with T→ G with C


DNA is essentially digital

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Bioinformatics

• Biomolecular computation→ idea: use biomolecules and biochemical

processes for solving computational problems

• Computational molecular biology→ goal: understand/explain biomolecular

systems and mechanisms


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After going through an age of specialization, the sciences are now reuniting into a common

mode of inquiry. “The next generation could

produce a scientist in the old sense, a real generalist.”

“Leonard Adleman”

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Biomolecular Computation

• Idea: use biomolecules and biochemical processes for solving computational problems

• Start point: Leonard Adleman, 1994→ solving the Hamilton Path Problem using

liquid-phase DNA chemistry

• Advantages:→ fast→ efficient in energy consumption→ great storage capabilities


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Computational Molecular Biology

• Goal: understand/explain biomolecular systems and mechanisms

• Application of computer technology to the management of biological information.

• Using Computers to gather, store, analyze and integrate biological and genetic information.


Bioinformatics

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Problems in Bioinformatics

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Sequencing GenomesAAACTGCTGACCGGTAACTGAGGCCTGCCTGCAATTGCTTAACTTGGC

GAGGGAACACAGTCTGCACACTCCTTCCGATAT

GAGGGAACACA

GTCTGCACACT

CCTTCCGATAT

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Sequencing GenomesAAACTGCTGACCGGTAACTGAGGCCTGCCTGCAATTGCTTAACTTGGC

GAGGGAACACAGTCTGCACACTCCTTCCGATAT

GAGGGAACACAGT

AGTCTGCACACTC

CTCCTTCCGATAT

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Sequencing Genomes

• Concrete problem: Sequence assembly problem→ given: fragments of large DNA sequence with

overlaps (multiple coverage)→ want: entire sequence

• Complicating factors→ computational complexity: can be seen as a

variation of shortest common superstring problem which is known to be NP-hard

→ incorrect/missing nucleotides in fragment data


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Relation btw Organisms

• Concrete problem: Phylogenetic tree inference→ given: homologous DNA sequence from multiple

species→ want: evolutionary tree relating these sequences

• Complicating factors→ errors in sequence→ complexity/quality of multiple sequence

alignment→ limited knowledge of evolutionary processes


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Sequence AlignmentAAACTGCTGACCGGTAACTGAGGCCTGCCTGCAATTGCTTAACTTGGC

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DNA-Genes-Proteins

• Basic molecule of life: directly controls the fundamental biology of life

• Proteins determines the biological makeup of humans or any living organisms

• Variations and errors in the genomic DNA may lead to different diseases or disorders


DNA → Genes → Proteins

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DNA → ProteinsAAACTGCTGACCGGTAACTGAGGCCTGCCTGCAATTGCTTAACTTGGC

DNA (gene)

↓mRNA

↓Protein

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Computational Gene Finding

• Given: raw sequence data• Predict:

→ coding and non-coding regions→ exons/introns→ splicing patterns→ transcription factors


Exon1

Exon2 Exon3

Intron1 Intron2

Exon1

Exon2 Exon3

Pre mRNA

mRNA

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Structure Prediction

• RNA & Protein• Minimum free energy• RNA structure:

→ primary structure: Single stranded sequence of A, U, G, C

→ secondary structure: Intra-molecular base pairs among its bases


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5’-GAGGGAACACAGUCUGCACACUCCUUC-3’

Secondary Structure

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Arc Diagram Representation

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LoopsAAACUGCUGACCGGUAACUGAGGCCUGCCUGCAAUUGCUUAACUUGGC

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27

Hairpin loop

Interior loop

Multi loopExternal loop

Bulge loopStacked pair

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Pseudoknotted Structure

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

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Str. Pred. Algorithms

• Dynamic programming algorithms→ restricted class of pseudoknotted structures→ Rivas and Eddy (R&E): O(N^6)

• Heuristic algorithms→ search over the solution space

AAACUGCUGACCGGUAACUGAGGCCUGCCUGCAAUUGCUUAACUUGGC

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Motif DiscoveryAAACTGCTGACCGGTAACTGAGGCCTGCCTGCAATTGCTTAACTTGGC

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Genes and Diseases

• Proteins perform all of life’s essential functions

• Changes in DNA sequence genome can have disastrous consequences


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Real World ApplicationsAAACTGCTGACCGGTAACTGAGGCCTGCCTGCAATTGCTTAACTTGGC

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Related Aspects

• Computation models of organisms or biological systems

• Nature-inspired algorithms→ genetic algorithms→ neural networks→ ant colony optimization

• Artificial life→ life-like behavior of artificial systems→ (re)-design or biological organisms


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Conclusion

• Bioinformatics: Using computers for gathering, storing and analyzing biological data

• Analyzing


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Thank you!AAACTGCTGACCGGTAACTGAGGCCTGCCTGCAATTGCTTAACTTGGC

Baharak Rastegari, [email protected]

Bio Informatics

mailto:[email protected]

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Genetic ProcessAAACTGCTGACCGGTAACTGAGGCCTGCCTGCAATTGCTTAACTTGGC

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DNA

• Gene expression?• Two genes


DNA → Genes → Proteins

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Genomic Sequence Data Interpretation

• Gene finding• Structure prediction• Pattern discovery• Classification • Clustering


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Understanding the Cell

• Concrete problem: Gene regulatory relationship inference→ given: expression profiles of two genes A, B→ want: decide if there is a (direct) regulatory

relationship between A and B, and whether its activating or inhibiting one

• Complicating factors→ imprecision/limitation in measuring expression

profiles→ indirect/complex regulatory relationship


1 Bio + Informatics AAACTGCTGACCGGTAACTGAGGCCTGCCTGCAATTGCTTAACTTGGC An Overview پرتال پرتال بيوانفورماتيك ايرانيان.

Documents

homologous dna sequence

sequence assembly problem

genomic dna

organismsconcrete problem

hamilton path problem

evolutionary tree

multiple species

biochemical processes