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question12-13.txt
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Question 12:
Steps:
go to: https://rest.ensembl.org/
Search for variation
choose: GET variation/:species/:id Uses a variant identifier (e.g. rsID) to return the variation features including optional genotype, phenotype and population data
Make query: 'https://rest.ensembl.org/variation/mouse/rs4224828?' -H 'Content-type:xml'
Look in results for "mappings: location"
curl 'https://rest.ensembl.org/variation/mouse/rs4224828?' -H 'Content-type:xml'
(Chose xml to increase readability in the terminal)
<html><title>EnsEMBL::REST</title><body><pre>---
MAF: ~
ambiguity: 'Y'
ancestral_allele: ~
evidence:
- Multiple_observations
- Frequency
mappings:
-
allele_string: T/C
assembly_name: GRCm38
coord_system: chromosome
end: 136443949
location: 4:136443949-136443949
seq_region_name: 4
start: 136443949
strand: 1
minor_allele: ~
most_severe_consequence: 3_prime_UTR_variant
name: rs4224828
source: Variants (including SNPs and indels) imported from dbSNP
synonyms: []
var_class: SNP
</pre></body></html>
=> answer: location: 4:136443949-136443949 (Chromosome 4, start: 136443949 end: 136443949)
Question 13:
Steps:
go to: https://rest.ensembl.org/
search for cross references
choose: GET xrefs/symbol/:species/:symbol Looks up an external symbol and returns all Ensembl objects linked to it. This can be a display name for a gene/transcript/translation, a synonym or an externally linked reference. If a gene's transcript is linked to the supplied symbol the service will return both gene and transcript (it supports transient links).
I happen to know that the zebrafish's scientific name is danio rerio, so I can perform the query is following:
curl 'https://rest.ensembl.org/xrefs/symbol/danio_rerio/MYCN?' -H 'Content-type:application/json'
Grab this ENS id: ENSDARG00000006837
Go to Sequence: GET sequence/id/:id Request multiple types of sequence by stable identifier. Supports feature masking and expand options.
Make query with ENS id
curl 'https://rest.ensembl.org/sequence/id/ENSDARG00000006837?type=genomic' -H 'Content-type:text/x-fasta'
Header says: chromosome:GRCz11:20:33294428:33299384:1
Go to sequence: GET sequence/region/:species/:region Returns the genomic sequence of the specified region of the given species. Supports feature masking and expand options.
Make query: (regionstart till regionstart+99)
curl 'https://rest.ensembl.org/sequence/region/danio_rerio/20:33294428..33294527:1?' -H 'Content-type:text/x-fasta'
>chromosome:GRCz11:20:33294428:33294527:1
TAGAATAATACTTCACAGCCCGAAACACAGAGGCGCAGAACAGTCTTCAGTCGCCGCGGT
AGATGTGCGACTCCAAACGGGAGGCACAGTGACTGCGATA