1. INTRODUCTION TO BIOLOGY AND BIOINFORMATICS
BIOINFORMATICS COURSE MTAT.03.239
11.09.2013 LIFE
Is a characteristic that distinguishes objects that have signaling and self-sustaining processes (i.e. living organism) to those that do not have it
Is a state of living characterized by capacity for metabolism, growth, reaction to stimuli, and reproduction
A diversity of life forms are found on Earth, eg. plants, animals, fungi, protists, archaea and bacteria
"Introduction to Bioinformatics" 2 Bioinformatics Course "Introduction to Bioinformatics" 3 Bioinformatics Course WHAT IS BIOLOGY ?
"Introduction to Bioinformatics" 4 Bioinformatics Course http://www.tagxedo.com/app.html "Introduction to Bioinformatics" 5 Bioinformatics Course BIOLOGY
Is a study of life and living organisms
It brings together the structure, function, growth, origin, distribution, adaptation, interactions, taxonomy and evolution of living organism
AEROBIOLOGY, AGRICULTURE, ANATOMY, ASTROBIOLOGY, BIOCHEMISTRY, BIOENGINEERING, BIOINFORMATICS, BIOMATHEMATICSOR, MATHEMATICAL BIOLOGY, BIOMECHANICS, BIOMEDICAL RESEARCH, BIOPHYSICS, BIOTECHNOLOGY, BUILDING BIOLOGY, BOTANY, CELLBIOLOGY, CONSERVATION BIOLOGY, CRYOBIOLOGY, DEVELOPMENTAL BIOLOGY, ECOLOGY, EMBRYOLOGY, ENTOMOLOGY, ENVIRONMENTAL BIOLOGY, EPIDEMIOLOGY, ETHOLOGY, EVOLUTIONARY BIOLOGY, GENETICS, HERPETOLOGY, HISTOLOGY, ICHTHYOLOGY, INTEGRATIVE BIOLOGY, LIMNOLOGY, MAMMALOGY, MARINE BIOLOGY, MICROBIOLOGY, MOLECULAR BIOLOGY, MYCOLOGY, NEUROBIOLOGY, OCEANOGRAPHY, ONCOLOGY, ORNITHOLOGY, POPULATION BIOLOGY, POPULATION ECOLOGY, POPULATION GENETICS, PALEONTOLOGY, PATHOBIOLOGY OR PATHOLOGY, PARASITOLOGY, PHARMACOLOGY, PHYSIOLOGY, PHYTOPATHOLOGY, PSYCHOBIOLOGY, SOCIOBIOLOGY, STRUCTURAL BIOLOGY, VIROLOGY
"Introduction to Bioinformatics" 6 Bioinformatics Course BIOLOGY
Is a study of life and living organisms
It brings together the structure, function, growth, origin, distribution, adaptation, interactions, taxonomy and evolution of living organism IOLOGY COMPRISES AREAS OF STUDY THAT FOCUS ON LIFE AT A B VARIETYAEROBIOLOGY ,OF AGRICULTURE LEVELS, ANATOMY AND, AFROMSTROBIOLOGY A , DIVERSITYBIOCHEMISTRY, B IOENGINEERINGOF PERSPECTIVES, BIOINFORMATICS , BIOMATHEMATICSOR, MATHEMATICAL BIOLOGY, BIOMECHANICS, BIOMEDICAL RESEARCH, BIOPHYSICS, BIOTECHNOLOGY, BUILDING BIOLOGY, BOTANY, CELLBIOLOGY, CONSERVATION BIOLOGY, CRYOBIOLOGY, DEVELOPMENTAL BIOLOGY, ECOLOGY, EMBRYOLOGY, ENTOMOLOGY, ENVIRONMENTAL BIOLOGY, EPIDEMIOLOGY, ETHOLOGY, EVOLUTIONARY BIOLOGY, GENETICS, HERPETOLOGY, HISTOLOGY, ICHTHYOLOGY, INTEGRATIVE BIOLOGY, LIMNOLOGY, MAMMALOGY, MARINE BIOLOGY, MICROBIOLOGY, MOLECULAR BIOLOGY, MYCOLOGY, NEUROBIOLOGY, OCEANOGRAPHY, ONCOLOGY, ORNITHOLOGY, POPULATION BIOLOGY, POPULATION ECOLOGY, POPULATION GENETICS, PALEONTOLOGY, PATHOBIOLOGY OR PATHOLOGY, PARASITOLOGY, PHARMACOLOGY, PHYSIOLOGY, PHYTOPATHOLOGY, PSYCHOBIOLOGY, SOCIOBIOLOGY, STRUCTURAL BIOLOGY, VIROLOGY
"Introduction to Bioinformatics" 7 Bioinformatics Course LIVING SYSTEMS
Domain - Eukaryota Kingdom - Animalia Phylum - Chordata Vertebrata (Subphylum) Class - Mammalia Order - Primates Anthropoidea (Suborder) Hominoidea (Superfamily) Family - Hominidae Genus - Homo Species - sapiens
"Introduction to Bioinformatics" 8 Bioinformatics Course HUMANS http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606 Lineage (full): root; cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Coelomata; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo; Homo sapiens "Introduction to Bioinformatics" 9 Bioinformatics Course SPECIES
Defined as a group of living organisms consisting of similar individuals capable of exchanging genes or interbreeding
http://www.nature.com/news/2011/110823/full/news.2011.498.html
"Introduction to Bioinformatics" 10 Bioinformatics Course
NO. OF SPECIES
http://www.iucnredlist.org/documents/summarystatistics/2010_1RL_Stats_Table_1.pdf
"Introduction to Bioinformatics" 13 Bioinformatics Course LEVELS OF ORGANISATION
http://www.nature.com/scitable/topicpage/biological-complexity-and-integrative-levels-of-organization-468 14 LEVELS OF ORGANISATION
http://www.nature.com/scitable/topicpage/biological-complexity-and-integrative-levels-of-organization-468 15 BIOLOGICAL QUESTIONS
How are all life-forms related? What was the first cell like? How do species adapt to their environment? Which part of our genome is evolving the fastest? Are we descendents of Neanderthals? What genes are responsible for major human disease? Why do we need new flu vaccines every day?
Introduction to Computational Biology, Nello Christiani and Matthew W. Hahn
"Introduction to Bioinformatics" 16 Bioinformatics Course BIOINFORMATICS ?
"Introduction to Bioinformatics" 17 Bioinformatics Course COMPUTER SCIENCE [CS] STUDIES COMPUTABLE PROCESSES
AND STRUCTURES ( WITH THE AID OF COMPUTERS )
"Introduction to Bioinformatics" 18 Bioinformatics Course BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
The boundaries between the two diciplines are not well defined and can be distinguished by the problems they solve
BIOINFORMATICS – is the application of statistics and computer science to the field of molecular biology
COMPUTATIONAL BIOLOGY – actual process of analyzing and interpreting data
"Introduction to Bioinformatics" 19 Bioinformatics Course DEFINITION OF BIOINFORMATICS
The term bioinformatics was coined in 1978 Bioinformatics is the application of information technology and computer science to the field of molecular biology The science of using / developing computer software and algorithms to record, analyze and merge biologically related data Using computer technology to manage large amounts of biological data Bioinformatics involves the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level
http://www.google.com/search?q=define%3ABioinformatics
"Introduction to Bioinformatics" 20 Bioinformatics Course DEFINITION OF BIOINFORMATICS
The collection, organization, storage, analysis, and integration of large amounts of biological data using networks of computers and databases Bioinformatics involves the integration of computers, software tools, and databases in an effort to address biological questions In summary, the use of computer science to solve biological problems
http://www.google.com/search?q=define%3ABioinformatics
"Introduction to Bioinformatics" 21 Bioinformatics Course BIOINFORMATIC FOCUS
MOLECULES
CELL TISSUE
ORGAN
ORGANISM
http://www.nature.com/scitable/topicpage/biological-complexity-and-integrative-levels-of-organization-468 22 BIOINFORMATIC FOCUS
MOLECULES
CELL TISSUE ANALYSIS AND INTERPRETATION OF VARIOUS TYPES OF BIOLOGICAL DATA INCLUDING: NUCLEOTIDE AND AMINO ACID SEQUENCES PROTEIN DOMAINS AND PROTEIN STRUCTURES , ORGAN , .
ORGANISM
http://www.nature.com/scitable/topicpage/biological-complexity-and-integrative-levels-of-organization-468 23 BIOINFORMATIC FOCUS
Development of new algorithms and statistics with which to assess biological information, such as relationships among members of large data sets.
http://www.nature.com/msb/journal/v3/n1/images/msb4100163-f4b.jpg "Introduction to Bioinformatics" 24 Bioinformatics Course BIOINFORMATIC FOCUS
Development and implementation of tools that enable efficient access and management of different types of information, such as various databases, integrated mapping information http://www.jofwidata.com/images/database-design-development.jpg http://wolfson.huji.ac.il/expression/detective.jpg "Introduction to Bioinformatics" 25 Bioinformatics Course UNITS OF INFORMATION IN BIOINFORMATICS
DNA Sequence Pathways
RNA Structure Interactions
Protein Evolution Mutations
"Introduction to Bioinformatics" 26 Bioinformatics Course UNITS OF INFORMATION IN COMPUTER SCIENCE File Storage capacity by Bits and Bytes
Bit Byte Kilobyte Megabyte Gigabyte 1024*8= 1024*8192= 1024*8388608= bit 1 8 8,192 8,388,608 8,589,934,592 1024*1024= 1024*1048576= byte 8 1 1024 1,048,576 1,073,741,824 Kilobyte 8,192 1024 1 KB 1024 1,048,576 Megabyte 8,388,608 1,048,576 1024 1 MB 1024
Gigabyte 8,589,934,592 1,073,741,824 1,048,576 1024 1 GB 8,796,093,022,208 Terabyte 1,099,511,627,776 1,073,741,824 1,048,576 1024 1TB 9,007,199,254,740,9 1,125,899,906,842, 1,099,511,627,77 1,073,741,824 1,048,576 Petabyte 90 620 6 1024 TB 1 PB
"Introduction to Bioinformatics" 27 Bioinformatics Course UNITS OF INFORMATION IN COMPUTER SCIENCE File Storage capacity by Bits and Bytes
Bit Byte Kilobyte Megabyte Gigabyte 9,007,199,254,740,99 1,125,899,906,84 1,099,511,627,77 1,073,741,824 1,048,576 Petabyte 0 2,620 6 1024 TB 1 BO 9,223,372,036,854,78 1,152,921,504,60 1,125,899,906,84 1,099,511,627,7 1,073,741,824 Exabyte 0,000 6,850,000 2,620 76 1,048,576 TB 1024 PB 1 EB 9,444,732,965,739,29 1,180,591,620,71 1,152,921,504,60 1,125,899,906,8 1,099,511,627,776 Zettabyte 0,000,000 7,410,000,000 6,850,000 42,620 1,073,741,824 TB 1,048,576 PB 1024 EB 1 ZB 1,208,925,819,61 9,671,406,556,917,030, 1,180,591,620,71 1,152,921,504,6 1,125,899,906,842,62 4,630,000,000,00 000,000,000 7,410,000,000 KB 06,850,000 MB 0 GB Yottabyte 0 1,099,511,627,776 TB 1,073,741,824 PB 1,048,576 EB 1024 ZB 1 YB
"Introduction to Bioinformatics" 28 Bioinformatics Course CELL SIZES
http://learn.genetics.utah.edu/content/begin/cells/scale/ "Introduction to Bioinformatics" 29 Bioinformatics Course HUMAN CELL
http://bhavanajagat.files.wordpress.com/2012/02/cell-structure-and-functions.jpg 30 EXAMPLES OF BIOLOGICAL DATA
GENOME – DNA TRANSCRIPTOME – RNA PROTEOME – Proteins
The biological information contained in a genome is encoded in deoxyribonucleic acid (DNA) or, for many types of virus, in ribonucleic acid (RNA)
"Introduction to Bioinformatics" 31 Bioinformatics Course NAME THE NUMBERS NUCLEUS DNA GENES CHROMOSOME 1 CELL 2
3 5 4
"Introduction to Bioinformatics" 32 Bioinformatics Course EXAMPLES OF BIOLOGICAL DATA
"Introduction to Bioinformatics" 33 Bioinformatics Course CENTRAL DOGMA OF MOLECULAR BIOLOGY
DNA is transcribed into RNA and RNA is translated into proteins
http://compbio.pbworks.com/f/central_dogma.jpg 34 CENTRAL DOGMA OF MOLECULAR BIOLOGY
http://www.uic.edu/classes/bios/bios100/lectures/centraldogma.jpg 35 EXAMPLES OF BIOLOGICAL DATA
GENOME – DNA TRANSCRIPTOME – RNA PROTEOME – Proteins
The biological information contained in a genome is encoded in deoxyribonucleic acid (DNA) or, for many types of virus, in ribonucleic acid (RNA)
"Introduction to Bioinformatics" 36 Bioinformatics Course GENOME
Is the entirety of an organism’s hereditary information
The genome includes both the genes and non-coding sequences of DNA/RNA
In 1995, Haemophilus influenzae or was the first genome of a living organism to be sequenced in July 1995
1 830 140 base pairs of DNA in single circular chromosome that contains 1740 protein-coding gene, 58 transfer RNA genes and 18 other RNA genes
http://www.sciencemag.org/content/269/5223/local/front-matter.pdf http://en.wikipedia.org/wiki/File:Haemophilus_influenzae_01.jpg
"Introduction to Bioinformatics" 37 Bioinformatics Course WHOLE GENOMES
"Introduction to Bioinformatics" 38 Bioinformatics Course GENOME SIZES
Introduction to Computational Biology, Nello Christiani and Matthew W. Hahn
"Introduction to Bioinformatics" 39 Bioinformatics Course GENOME SIZES
Japanese flower Paris japonica 130 billion base pairs – 50 times the human genome
"Introduction to Bioinformatics" 40 Bioinformatics Course COMPLETELY SEQUENCED GENOMES
"Introduction to Bioinformatics" 41 Bioinformatics Course HUMAN GENOME
One cell DNA
• 23 pairs of • 3 billion pairs chromosomes of DNA bases
RNA
• ≈21,000 to Human 23,000 body genes Protein • 1014 cells • (100 • ≈100 000 trillion) different proteins
"Introduction to Bioinformatics" 42 Bioinformatics Course Relative proportions (%) of bases in DNA
CURRENT SCIENCE, VOL. 85, NO. 11, 10 DECEMBER 2003
"Introduction to Bioinformatics" 43 Bioinformatics Course DNA
DNA with high GC-content is more stable than DNA with low GC-content, 3 hydrogen bonds
"Introduction to Bioinformatics" 44 Bioinformatics Course DNA vs RNA
DNA – deoxyribonucleic acid RNA –ribonucleic acid Sugar is deoxyribose Sugar is ribose DNA is a polymer of RNA is a polymer of deoxyribonucleotides ribonucleotides Bases are adenine (A), Bases are adenine (A), guanine (G), cytosine (C) and guanine (G), cytosine (C) and thymine (T) uracil (U)
http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Images3/dna_rna1.gif 45 DNA SEQUENCE
Raw DNA sequence Coding or non-coding Parses into genes 4 nucleotide bases ATGC
>ENST00000539570 cdna:known chromosome:GRCh37:15:63889592:63893885:1 gene:ENSG00000259662 gene_biotype:protein_coding transcript_biotype:protein_coding ATGTGGCCACTGCTCACCATGCACATAACCCAGCTCAACCGGGAGTGCCTGCTGCACCTCTTCTCCTTCCTA GACAAGGACAGCAGGAAGAGCCTTGCCAGGACCTGCTCCCAGCTCCACGACGTGTTTGAGGACCCCGCA CTCTGGTCCCTGCTGCACTTCCGTTCCCTCACTGAACTCCAGAAGGACAACTTCCTCCTGGGCCCGGCACTC CGCAGCCTCTCCATCTGCTGGCACTCCAGCCGCGTGCAGGTGTGCAGCATTGAGGACTGGCTCAAGAGTG CCTTCCAGAGAAGCATCTGCAGCCGGCACGAGAGCCTGGTCAATGATTTCCTCCTCCGGGTGTGCGACAG GCTTTCTGCTGTGCGCTCCCCACGGAGGCGGGAGGCGCCTGCACCGTCCTCGGGGACTCCGATCGCCGTT GGACCGAAATCACCTCGGTGGGGAGGACCTGACCACTCGGAGTTCGCCGACTTGCGCTCGGGGGTGACG GGGGCCAGGGCTGCCGCGCGCAGGGGTCTGGGGAGCCTCCGGGCGGAGCGACCCAGCGAGACCCCGC CGGCTCCCGGAGTGTCCTGGGGACCGCCACCTCCAGGAGCCCCGGTGGTGATCTCGGTGAAGCAGGAGG AGGGGAAGCAGGGGCGCACGGGCAGAAGGAGCCACCGAGCCGCTCCTCCTTGCGGTTTTGCCCGCACG CGCGTCTGCCCGCCCACCTTTCCTGGGGCGGATGCGTTCCCGCAGTGA
"Introduction to Bioinformatics" 46 Bioinformatics Course A GENE
http://www.down-syndrome.org/updates/2054/updates-2054-figure1-400w.png
"Introduction to Bioinformatics" 47 Bioinformatics Course GENE EXPRESSION REGULATORS
http://www.nature.com/scitable/topicpage/gene-expression-14121669
"Introduction to Bioinformatics" 48 Bioinformatics Course GENE EXPRESSION REGULATORS - EPIGENETICS
http://scienceblogs.com/pharyngula/2008/07/22/epigenetics/
"Introduction to Bioinformatics" 49 Bioinformatics Course EXAMPLES OF BIOLOGICAL DATA
GENOME – DNA TRANSCRIPTOME – RNA PROTEOME – Proteins
Transcriptome is a set of all RNA molecules including mRNA, rRNA, tRNA, and non- coding RNA produced in one or a population of cells
http://www.bio.miami.edu/~cmallery/150/gene/c7.17.7b.transcription.jpg
"Introduction to Bioinformatics" 50 Bioinformatics Course TRANSCRIPTION
http://www.youtube.com/watch?v=ztPkv7wc3yU
"Introduction to Bioinformatics" 51 Bioinformatics Course TRANSCRIPTION
http://www.bio.miami.edu/~cmallery/150/gene/c7.17.7b.transcription.jpg
"Introduction to Bioinformatics" 52 Bioinformatics Course ALTERNATIVE SPLICING
http://www.nature.com/scitable/content/a-schematic-representation-of-alternative-splicing-95777
"Introduction to Bioinformatics" 53 Bioinformatics Course TYPES OF RNA
mRNA – messenger RNA: encodes amino acid sequences of a polypeptide tRNA – transfer RNA: brings amino acids to ribosomes during translation rRNA – ribosomal RNA: with ribosome proteins makes up the ribosomes, the organelles that translate the mRNA snRNA – small nuclear RNA: forms complexes with proteins that are used in RNA processing in eukaryotes
http://csls-text.c.u-tokyo.ac.jp/images/fig/fig03_4.gif
"Introduction to Bioinformatics" 54 Bioinformatics Course TYPES OF RNA
http://finchtalk.geospiza.com/2009_05_01_archive.html
"Introduction to Bioinformatics" 55 Bioinformatics Course EXAMPLES OF BIOLOGICAL DATA
GENOME – DNA TRANSCRIPTOME – RNA PROTEOME – Proteins
The proteome is the entire set of proteins expressed by a genome, cell, tissue or organism.
http://artavanis-tsakonas.med.harvard.edu/research_images/figure_harsha_proteome.jpg
"Introduction to Bioinformatics" 56 Bioinformatics Course FROM TRANSCRIPTION TO TRANSLATION
http://www1.cs.columbia.edu/~cleslie/cs4761/microarray/central-dogma.png
"Introduction to Bioinformatics" 57 Bioinformatics Course TRANSLATION
http://0.tqn.com/d/chemistry/1/0/G/m/mrnatranslation.jpg
"Introduction to Bioinformatics" 58 Bioinformatics Course TRANSLATION INITIATION
http://bioap.wikispaces.com/Ch+17+Collaboration
"Introduction to Bioinformatics" 59 Bioinformatics Course TRANSLATION TERMINATION
http://kvhs.nbed.nb.ca/gallant/biology/translation_termination.html
"Introduction to Bioinformatics" 60 Bioinformatics Course UNIVERSAL GENETIC CODE
http://www.biogem.org/codon.jpg
"Introduction to Bioinformatics" 61 Bioinformatics Course AMINO ACIDS
62 PROTEIN
Proteins consists of long chains of amino acid sequences 20 letter alphabet (IUPAC nomenclature)
IUPAC amino Three letter IUPAC amino Three letter Amino acid Amino acid acid code code acid code code A Ala Alanine M Met Methionine C Cys Cysteine N Asn Asparagine D Asp Aspartic Acid P Pro Proline E Glu Glutamic Acid Q Gln Glutamine F Phe Phenylalanine R Arg Arginine G Gly Glycine S Ser Serine H His Histidine T Thr Threonine I Ile Isoleucine V Val Valine K Lys Lysine W Trp Tryptophan L Leu Leucine Y Tyr Tyrosine "Introduction to Bioinformatics" 63 Bioinformatics Course PROTEIN SEQUENCE
>sp|P48431|SOX2_HUMAN Transcription factor SOX-2 OS=Homo sapiens GN=SOX2 PE=1 SV=1 MYNMMETELKPPGPQQTSGGGGGNSTAAAAGGNQKNSPDRVKRPMNAFMVWSRGQRRKMA QENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKTLM KKDKYTLPGGLLAPGGNSMASGVGVGAGLGAGVNQRMDSYAHMNGWSNGSYSMMQDQLGY PQHPGLNAHGAAQMQPMHRYDVSALQYNSMTSSQTYMNGSPTYSMSYSQQGTPGMALGSM GSVVKSEASSSPPVVTSSSHSRAPCQAGDLRDMISMYLPGAEVPEPAAPSRLHMSQHYQS GPVPGTAINGTLPLSHM
"Introduction to Bioinformatics" 64 Bioinformatics Course PROTEIN SIZE
http://www.quora.com/Protein-nutrition-1/Whats-the-average-size-of-a-human-protein-in-kDa
65 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1150220/ PROTEIN STRUCTURE
67 http://upload.wikimedia.org/wikipedia/commons/thumb/0/05/Protein_structure.png/1024px-Protein_structure.png PROTEIN DOMAINS
68 PROTEIN SEQUENCE
Proteins are divided into domains
>sp|P48431|SOX2_HUMAN Transcription factor SOX-2 OS=Homo sapiens GN=SOX2 PE=1 SV=1 MYNMMETELKPPGPQQTSGGGGGNSTAAAAGGNQKNSPDRVKRPMNAFMVWSRGQRRKMA QENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKTLM KKDKYTLPGGLLAPGGNSMASGVGVGAGLGAGVNQRMDSYAHMNGWSNGSYSMMQDQLGY PQHPGLNAHGAAQMQPMHRYDVSALQYNSMTSSQTYMNGSPTYSMSYSQQGTPGMALGSM GSVVKSEASSSPPVVTSSSHSRAPCQAGDLRDMISMYLPGAEVPEPAAPSRLHMSQHYQS GPVPGTAINGTLPLSHM DNA BINDING DOMAIN
http://www.uniprot.org/ 69 GENE TRANSCRIPTION, TRANSLATION AND PROTEIN SYNTHESIS
70 http://compbio.pbworks.com/f/central_dogma.jpg CENTRAL DOGMA
71 BIOINFORMATIC APPLICATIONS
The integrative approaches are useful and applied in Agricultural Higher yield in crops or fruits Disease or drought resistance crops Medical To understand processes in healthy and disease individuals Genetic diseases Pharmaceutical To find or develop new and better drugs Gene based drugs Structure based drug designing
"Introduction to Bioinformatics" 72 Bioinformatics Course BIOINFORMATIC QUESTIONS 1
To identify an unknown gene of interest Sequence matching Is there a match to known sequence in the database Which protein family does it match to How to identify more family members I have an similar structure, how to identify its potential ligands How to identify if my gene/protein is found present also in other species How can I identify genes that are inherited together in a specific region
"Introduction to Bioinformatics" 73 Bioinformatics Course BIOINFORMATIC QUESTIONS 2
I have to constructed a artificial gene, how do I design the primers, how to check if I have the right sequence? To know structure of an poorly expressed RNA sequence To identify the structure and function of a protein sequence To cluster protein sequences into families of related sequences and develop models To generate phylogenetic trees to identify the evolutionary relationships using similar proteins/DNA To identify which other proteins interacts with sequence of interest.
"Introduction to Bioinformatics" 74 Bioinformatics Course BIOINFORMATIC QUESTIONS 3
Find genes that have similar expression in specific conditions Find transcription factors that regulate specific genes Vizualise different gene and protein networks Describe the regulation of genes
"Introduction to Bioinformatics" 75 Bioinformatics Course