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systeembiologie samenvatting deeltentamen 1
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College aantekeningen van systeembiologie deel 1. Alle colleges zijn hierin verwerkt, alles wat op het tentamen kwam stond hier in.
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By: thibaudtegroen • 6 year ago
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Hoofdstuk 1DNA sequenties zijn opgeslagen in fasta files. .faa, .fna, .fasta, .fa
Preferred extension for protein is .faa (Fasta Amino Acid)
Preferred extension for DNA fasta files is .fna (Fasta Nucleic Acid)
Verschillende letters in de verschillende files.
In DNA file:
N = we weten niet welke letter, maar geen gap
In eiwit file:
X = we weten niet welke letter, maar geen gap
Metadata
Naam van het organisme
Research Group that generated the sequence
Geographic coordinates and date/time the sample was collected
Environment (biome)
Methods like nucleid acid extraction protocol, DNA sequencing technology
Genbank formaat is het formaat waarin veel hiervan wordt opgeslagen
Hierin staat ook waar het is gepubliceerd.
Van niet alle sequenties zijn de functies bekend, hier wordt dan de label ‘hypothetical’ aan gehangen.
Error propagation
- mensen kunnen fouten maken
- computers kunnen deze fouten overnemen
- Dit is error propagation
,Scientific literature databases
- pubmed/google scholar
Hier kan je ook in zoeken naar key words
Using databases in biology
Als je een database gebruikt moet je opschrijven op welke datum je dat hebt gedaan, want deze
veranderen elke dag.
De identifiers moet je meenemen in je publicatie
In artikel:
- cite the article
- note the namen, version number, and/or date
- list de Identifiers
People are mostly interested in:
1. Themselves
2. Their food
3. Their diseases
Hier is dus ook de meeste data over.
Genoom: alle genen
Genomics: studie van alle genen
Transcriptomics: studie van alle RNA transcripten
Proteoom: studie van alle eiwitten
Microbioom: alle micro-organismen in een bepaald milieu
, First generation
- Chain termination sequencing
o Sanger
Second generation
- Massively parallel sequencing
o Illumina (MiSeq)
o Ion Torrent
Third generation
- Single molecule sequencing
o Oxford Nanopore (MinION)
o Pacific Biosciences (PacBio)
Data sharing kan gewoon via internet, heel belangrijk om je resultaten te delen.
Bioinformatici gebruiken data op 2 verschillende manieren,
1. Given a biological question, a good bioinformatician will immediately think about which
datasets could be used to answer it.
2. Given a dataset, a good bioinformaticion will immediately think about which new biological
question it could answer.
Viroom: alle virussen
Assembleren: kleine reads samenvoegen tot grotere contigs
Door het gebruik te maken van een database beïnvloed je misschien je resultaten. Want deze zijn
biased, van sommige organismen is heel erg veel bekend en van sommige nog niks.
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