De aantekeningen van hoorcollege 1 over Introduction + homology searching van het vak introduction to bioinformatics. Het document bevat duidelijke afbeeldingen. Verder is het overzichtelijk en duidelijk gemarkeerd.
Introduction to bioinformatics
Hoorcollege 1 – 8 januari 2024
Introduction + homology searching
Human genome:
- 23 pairs of chromosomes (DNA)
o DNA codes for genes
- 20,000 genes on DNA and 20,000 proteins
o 1.5% of DNA is protein/gene coding
- 3 billion base pairs
- 37 trillion cells
Measure cells measure a lot of things
What is bioinformatics used for?
- DNA sequencing
We can sequence the whole human DNA
We get lots of data
Identify pinpoint mutations / changes
Bioinformatics is used ‘to find the needle in the haystack’ = naald in hooiberg
But what does the needle do is more important
- What does the mutation mean
- What is the effect of the mutation? Is it related to the disease?
DNA sequencing analysis
Images translated to letters reads (short DNA sequences) aligned reads
mutations
Each step contains bioinformatics
Bioinformatics develop methods, create workflows, and analyze large datasets to answer
biological questions
- For example, develop new algorithm to align proteins
- Typically, many computational methods need to be combined in a workflow to
process all data
“Omics” analysis in biomedicine
= Data science in the field of molecular biology
Omics data = extensive molecular profiling data of biological sample
, Do this for all / many proteins in the cell
- Measure (levels of) molecules/variant in cells
- Huge number of measurements per sample (>1000)
o Important
- For example
o All bases of the DNA
o mRNA abundances of all genes
o abundances of many/all proteins
What can we measure, and how?
Some examples, are much more
Genomics (DNA)
- point mutations (1 letter) / small variants
- structural variant (bigger changes – cancer)
- methylation
- DNAseq
- chemical marks … eppi/???
Transcription (mRNA)
- single cell RNAseq
- micro arrays (becoming obsolete)
proteomics (proteins)
- measure proteins
- immunohistochemistry
o empty body’s
- mass spectrometry (MS)
o high throughput
metabolomics (metabolites / small molecules)
- NMR / mass spectrometry
Can now measure individual cells ?
Personalized medicine = which patient should (not) get drug based on (molecular) profiling
of patient
Biomarkers are indicators of some biological state or condition
Omics data is often used to find biomarkers
Examples of biomarkers:
- A metabolite or protein present in blood/urine/stool
- Mutation found in blood or a tumor sample
- Overexpression of specific gene or set of genes in diseased tissue (from RNAseq)
Los beneficios de comprar resúmenes en Stuvia estan en línea:
Garantiza la calidad de los comentarios
Compradores de Stuvia evaluaron más de 700.000 resúmenes. Así estas seguro que compras los mejores documentos!
Compra fácil y rápido
Puedes pagar rápidamente y en una vez con iDeal, tarjeta de crédito o con tu crédito de Stuvia. Sin tener que hacerte miembro.
Enfócate en lo más importante
Tus compañeros escriben los resúmenes. Por eso tienes la seguridad que tienes un resumen actual y confiable.
Así llegas a la conclusión rapidamente!
Preguntas frecuentes
What do I get when I buy this document?
You get a PDF, available immediately after your purchase. The purchased document is accessible anytime, anywhere and indefinitely through your profile.
100% de satisfacción garantizada: ¿Cómo funciona?
Nuestra garantía de satisfacción le asegura que siempre encontrará un documento de estudio a tu medida. Tu rellenas un formulario y nuestro equipo de atención al cliente se encarga del resto.
Who am I buying this summary from?
Stuvia is a marketplace, so you are not buying this document from us, but from seller dboone264. Stuvia facilitates payment to the seller.
Will I be stuck with a subscription?
No, you only buy this summary for $4.88. You're not tied to anything after your purchase.
