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Data Mining - Biological data analysis Lecture 2

DNA, RNA and flow of information, RNA sequences have Structure, Packag...

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Data Mining

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Assiut University

Academic year: 2023/2024

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Data Mining Concepts

Bio Mining- Lecture 6 : Biological Data Analysis II

Topics

- We will explore the syllabus

through a series of questions?

- Please ASK

- All logistical information will be

given at the end

A gene is expressed in two steps 1- Transcription: RNA synthesis 2- Translation: Protein synthesis
What is a gene?

A gene is a unit of heredity that is responsible for the transmission of traits from parents to offspring. It is a segment of DNA that contains the instructions for building and maintaining an organism. Genes determine various characteristics such as eye color, height, and susceptibility to certain diseases. They can also be

mutated, leading to genetic disorders or variations in traits.

How would you find genes in genomic sequence?

Gene location by sequence inspection. Sequence inspection can be used to locate genes because genes are not random series of nucleotides but instead have distinctive features. These features determine whether a sequence is a gene or not, and so by definition are not possessed by non-coding DNA.

Quiz:Transcription?

What causes transcription to switch on or off? How can we find transcription factor binding sites?
The number of transcripts of a gene is indicative of the activity of the gene. Can we count the number of transcripts? Can we tell if the number of copies is abnormally high, or abnormally low?

Quiz: Translation

How is Protein Sequencing done?

The two major direct methods of protein sequencing are mass spectrometry and Edman degradation using a protein sequenator (sequencer). Mass spectrometry methods are now the most widely used for protein sequencing and identification but Edman degradation remains a valuable tool for characterizing a protein's N-terminus.

Are all genes translated?

Not all genes are transcribed all the time. Instead, transcription is controlled individually for each gene (or, in bacteria, for small groups of genes that are transcribed together). Cells carefully regulate transcription, transcribing just the genes whose products are needed at a particular moment.

What is special about RNA?

RNA is a unique polymer. Like DNA, it can bind with great specificity to either DNA or another RNA through complementary base pairing. It can also bind specific proteins or small molecules, and, remarkably, RNA can catalyze chemical reactions, including joining amino acids to make proteins.

Can you predict non-coding genes in the genome? Can you predict structure for RNA?

Quiz:RNA

- How can you predict secondary,

and tertiary structure of RNA?

- Given an RNA query (sequence

+ structure), can you find

structural homologs in a

database? EX: tRNA

Packaging

All of the transcripts are encoded in DNA, which is packaged into the genome.
Many databases (much of sequence) are devoted to storing entire genomic sequences.

Quiz: Sequencing

Suppose you have fragments, and you want to assemble them into the genome, how would you do it? - How would you determine the overlaps - Layout, Consensus?

Quiz:Population genetics

- We are all similar, yet we are

different. How substantial are

the differences?

Why are some people more likely to get a disease then others?
If you had DNA from many sub- populations, Asian, European, African, can you separate them?
How is disease gene mapping done?

based on the nucleotide

sequences of certain regions of

human DNA that are unique to

individuals. DNA fingerprinting is

used in a variety of situations,

such as criminal investigations,

other forensic purposes and

paternity testing. In these

situations, one aims to “match”

two DNA fingerprints with one

another, such as a DNA sample

from a known person and one

from an unknown person.

- What can you study with these

variations?

How do these individual

differences occur?

- Mutation

Recombination

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