Samenvatting Bioinformatica (TLSC-BID3V-17_2020)

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

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,Visualiseren van genomische data................................................................................................21




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, Handige links
NCBI:
https://www.ncbi.nlm.nih.gov/

BLAST:
https://blast.ncbi.nlm.nih.gov/Blast.cgi

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




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