1. Introduction to Bioinformatics
DNA -> RNA -> Proteins
DNA-
• Genes
• Introns/exons
• Chromosomes
• Genome
• Nuclear
• Mitochondria
RNA-
• ORF
• Coding region
• mRNA
• Codon
Protein-
• Secondary- 2^0
• Tertiary- 3^0
• Structure
• Crystal
• Catalytic site
Reading list
1. Molecular Biology of the Cell http://www.ncbi.nlm.nih.gov/books/NBK21054/
2. Molecular Cell Biology http://www.ncbi.nlm.nih.gov/books/NBK21475/
Genome resource database and web
These databases help understand:
→ How is the gene sequenced?
→ How is a genome sequenced?
Bioinformatics- BLGY2201 Page 1
,Sanger sequencing- add fluorescent tags in PCR when amplifying a DNA sequence, the different colours gives an
indication to the sequence of the DNA.
However there are places where were not 100% certain
Databases are growing exponentially- >100 gigabases
→ Bibliographic- MedLine
→ Amino acid Seq- SWISS-PROT
→ 3D molecular structure- PDB
→ Nucleotide seq- GenBank, EMBL
→ Biochemical pathways- KEGG, WIT
→ Motif libraries- PROSITE, Blocks
These are some examples for databases
The graph shows the rapid increase in databases and bioinformatic tools allowing DNA sequencing
DNA data projects for specific purposes
* 1000 genomes project- 1000 peoples genomes sequenced
* Genome 10k project- sequence 10,000 vertebrate genomes
* Metagenomics- environmental samples like skin, digestive tract, soil
* Paleogenetics- ancient DNA such as history of man, Neanderthal DNA
Size of genome
Bioinformatics- BLGY2201 Page 2
,There are different services out there, e.g. can tell your ancestry by taking a sample.
RNA and cDNA can be sequence as RNA is converted to cDNA.
e.g. below Is coding sequence for human clotting factor IX gene
We find the beginning and of gene after finding the ATG start codon and one of 3 stop codons:
• TAA
• TGA
• TAG
Its rare a gene doesn’t start with ATG- 90% of all genes (methionine)
Can reformat the same gene as triplets.so we can view the coding region of the protein and translate them to amino
acids.
Bioinformatics- BLGY2201 Page 3
, Can get the single letter code.
A single base change causes haemophilia- enough to inactive protein factor IX and prevent proper clotting. Most
single base changes don’t cause a big change due to redundancy. If mutation is in the third base, a big possibility
that it is the same amino acids.
Bioinformatics- BLGY2201 Page 4
DNA -> RNA -> Proteins
DNA-
• Genes
• Introns/exons
• Chromosomes
• Genome
• Nuclear
• Mitochondria
RNA-
• ORF
• Coding region
• mRNA
• Codon
Protein-
• Secondary- 2^0
• Tertiary- 3^0
• Structure
• Crystal
• Catalytic site
Reading list
1. Molecular Biology of the Cell http://www.ncbi.nlm.nih.gov/books/NBK21054/
2. Molecular Cell Biology http://www.ncbi.nlm.nih.gov/books/NBK21475/
Genome resource database and web
These databases help understand:
→ How is the gene sequenced?
→ How is a genome sequenced?
Bioinformatics- BLGY2201 Page 1
,Sanger sequencing- add fluorescent tags in PCR when amplifying a DNA sequence, the different colours gives an
indication to the sequence of the DNA.
However there are places where were not 100% certain
Databases are growing exponentially- >100 gigabases
→ Bibliographic- MedLine
→ Amino acid Seq- SWISS-PROT
→ 3D molecular structure- PDB
→ Nucleotide seq- GenBank, EMBL
→ Biochemical pathways- KEGG, WIT
→ Motif libraries- PROSITE, Blocks
These are some examples for databases
The graph shows the rapid increase in databases and bioinformatic tools allowing DNA sequencing
DNA data projects for specific purposes
* 1000 genomes project- 1000 peoples genomes sequenced
* Genome 10k project- sequence 10,000 vertebrate genomes
* Metagenomics- environmental samples like skin, digestive tract, soil
* Paleogenetics- ancient DNA such as history of man, Neanderthal DNA
Size of genome
Bioinformatics- BLGY2201 Page 2
,There are different services out there, e.g. can tell your ancestry by taking a sample.
RNA and cDNA can be sequence as RNA is converted to cDNA.
e.g. below Is coding sequence for human clotting factor IX gene
We find the beginning and of gene after finding the ATG start codon and one of 3 stop codons:
• TAA
• TGA
• TAG
Its rare a gene doesn’t start with ATG- 90% of all genes (methionine)
Can reformat the same gene as triplets.so we can view the coding region of the protein and translate them to amino
acids.
Bioinformatics- BLGY2201 Page 3
, Can get the single letter code.
A single base change causes haemophilia- enough to inactive protein factor IX and prevent proper clotting. Most
single base changes don’t cause a big change due to redundancy. If mutation is in the third base, a big possibility
that it is the same amino acids.
Bioinformatics- BLGY2201 Page 4
