Samenvatting van het vak Bioinformatica uit de opleiding life sciences, ook wel biologie en medisch laboratoriumonderzoek. Per onderwerp zijn de leerdoelen uitgewerkt aan de hand van de canvaspagina en de opdrachten. De onderwerpen zijn puntsgewijs samengevat, om zo een goed overzicht te krijgen. D...
Contents
Handige links..........................................................................................................................................3
Extra’s.....................................................................................................................................................4
Elementen van het eukaryote genoom..........................................................................................4
Script schrijven...............................................................................................................................4
Les 1 De onbekende bacterie.................................................................................................................5
Les 2 De bekende bacterie......................................................................................................................5
Blast analyse...................................................................................................................................5
Ontwerpen van primers voor kloneren..........................................................................................6
Les 3 Het eukaryote genoom..................................................................................................................7
Transcript varianten.......................................................................................................................7
Ontwerpen van primers voor gen expressie analyse......................................................................7
Mutaties.........................................................................................................................................8
Les 4 De grote vriendelijke server..........................................................................................................8
Maken van een stappenplan voor een script..................................................................................8
Linux omgeving en functies............................................................................................................9
Mutatie analyse............................................................................................................................11
Les 5 Knippen en plakken met DNA......................................................................................................12
Splicing..........................................................................................................................................12
UCSC browser...............................................................................................................................12
Les 6 De eiwit code...............................................................................................................................13
Eiwit Translatie.............................................................................................................................13
Eiwit BLAST en eiwit domeinen....................................................................................................14
Mutaties.......................................................................................................................................14
Les 7 Mutatie analyse...........................................................................................................................14
Bash Analyse Pipeline...................................................................................................................14
Les 8 Moleculaire pathways.................................................................................................................16
Molecular Pathways.....................................................................................................................16
Kegg databank..............................................................................................................................16
Les 9 De histone code...........................................................................................................................18
Post-translational modification (PMTs), Histonen, Histon code...................................................18
Uniprot databank..........................................................................................................................20
Les 10 Eiwit-DNA interacties.................................................................................................................20
BED bestanden.............................................................................................................................20
Verkrijgen van DNA sequenties via ECSC Genome browser.........................................................20
1
,Visualiseren van genomische data................................................................................................21
Sequentie van 3’-5’ naar 5’-3’ maken:
http://www.bioinformatics.org/sms/rev_comp.html
Ontwerpen van primers:
https://www.ncbi.nlm.nih.gov/tools/primer-blast/
Algemene achtergrond informatie over Perl:
https://learn.perl.org/
https://bioperl.org/
Linux commands:
https://ss64.com/bash/
http://www.gnu.org/software/coreutils/coreutils.html
UCSC:
http://genome.ucsc.edu/
Translatie:
https://www.ebi.ac.uk/services
Berekenen moleculair gewicht en iso-elektrisch punt:
https://web.expasy.org/compute_pi/
NCBI Pubmed:
https://pubmed.ncbi.nlm.nih.gov/
Kegg:
https://www.kegg.jp/
UniProt:
https://www.uniprot.org/
Lengte van ieder humaan chromosoom:
https://www.ncbi.nlm.nih.gov/grc/human/data
3
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