Dit bestand bevat links naar de websites gebruikt in de les en de syntax gebruikt in jupyter (wel niet van het gedeelte van python)
Ik persoonlijk heb gewoon dit document gebruikt tijdens het oefenen thuis en dan op het openboek examen had ik genoeg tijd omdat ik alles hier snel in terug kon vinde...
Websites, links en syntax
Websites en links
https://www.ncbi.nlm.nih.gov/
=entrez gene
FASTA RefSeq, NM_, Nucleotide, Genbank format, Text editor, genexpressie
RefSeq_id = NM… of NP…
https://www.ebi.ac.uk/ena/browser/home
= europees alternatief van genbank
EMBL formaat
DBfetch
https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ena_sequence&id=L07770&style=raw
geeft rechtstreeks alle informatie van id
id nog aanpassen
https://www.ensembl.org/index.html
gencode annotatie
ENSG: gen-id
ENST: transcript-id
Ortholoog en paraloog predicties
Biomart: lijsten
Ook bv van genenlijst de sequenties downloaden
http://www.openhelix.com/
https://genome.ucsc.edu/
= ucsc
Bv exonen
http://obofoundry.org/
open biomedical ontology
https://www.omim.org/
genetische varianten en hun effecten
https://www.ebi.ac.uk/QuickGO/annotations
gene ontology en annotaties
https://www.informatics.jax.org/
alles van de muis
https://rgd.mcw.edu/
alles van de rat
https://wormbase.org//#012-34-5
alles van de worm
https://zfin.org/
alles van de zebravis
https://www.yeastgenome.org/
alles van gist
https://bio.tools/ecogene
alles van E. coli
https://www.omim.org/
ziektes, phenotypes
sequelpro login
hostname: genome-mysql.cse.ucsc.edu
username: genome
zonder wachtwoord
https://cells.ucsc.edu/
ucsc cell browser
genen van celsoorten vinden
downloaden als gzipt
https://biit.cs.ut.ee/gprofiler/gost
gprofiler
lijst van namen omzetten tot bv alle refseq
functional profiling (data sources, berekent kansen)
functies van genen/cellen te weten komen
Syntax
Opslaan: ctrl s
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