Moderator: Emily_Ensembl

gravatar for Emily_Ensembl
Emily_Ensembl14k
Reputation:
13,550
Status:
Trusted
Location:
EMBL-EBI
Website:
http://www.ensembl.org...
Twitter:
@Ensemily
Last seen:
an hour ago
Joined:
4 years, 10 months ago
Email:
e***********@gmail.com

Outreach Project Leader for Ensembl. I can help you with anything Ensembl-related (or find someone who can).

Posts by Emily_Ensembl

<prev • 883 results • page 1 of 89 • next >
0
votes
1
answer
109
views
1
answers
Answer: A: Reference genome for wheat/ Triticum aestivum
... The latest wheat genome consists of a number of scaffolds. Where it is known which chromosome the scaffold belongs to, they contain the chromosome in the scaffold name, for example the scaffold TGACv1_scaffold_250239_3DL is part of chromosome 3DL. There is more information about the assembly here: h ...
written 12 days ago by Emily_Ensembl14k
2
votes
1
answer
143
views
1
answers
Answer: A: VEP ENSEMBL unexpected output when considering vcf insertions.
... @WouterDeCoster is right. The allele column will report the forward strand, the codons column will report the strand of the transcript that is hit, which may be the forward or reverse strand. This means that around half the time, the base in the codons column will be the complement of the base in th ...
written 12 days ago by Emily_Ensembl14k
1
vote
1
answer
242
views
1
answers
Comment: C: how can I get supporting evidence for each transcript in Ensembl?
... The transcript supporting evidence is found in the [Transcript_supporting_feature][1] table, the exon supporting evidence is found in the [supporting_feature][2] table. [1]: http://www.ensembl.org/info/docs/api/core/core_schema.html#transcript_supporting_feature [2]: http://www.ensembl.org/inf ...
written 13 days ago by Emily_Ensembl14k
2
votes
1
answer
159
views
1
answers
Answer: A: Finding orthologs and sequences from BioMart
... BioMart will allow you to get the sequences for the orthologues if you combine two queries. There are instructions on how to do this here: http://www.ensembl.org/info/data/biomart/biomart_combining_species_datasets.html ...
written 14 days ago by Emily_Ensembl14k
2
votes
1
answer
242
views
1
answers
Answer: A: how can I get supporting evidence for each transcript in Ensembl?
... The supporting evidence is available for each transcript, if you go to [Supporting evidence][1] on the transcript page. These data are not available in BioMart. If you're looking to get these data on a large scale, you would need to look at using our Perl API, or querying the MySQL tables. I will c ...
written 14 days ago by Emily_Ensembl14k
3
votes
1
answer
93
views
1
answers
Answer: A: Access old version of ensembl via rest API
... There are no archives on the REST API at the moment. Only the current database is accessible. You can get archive data via the Perl API by using the software version matched to the database version you want to access. ...
written 19 days ago by Emily_Ensembl14k
0
votes
0
answers
101
views
0
answers
Comment: C: Reannotete/Compare data between ensembl releases but within the same assembly
... Hello mgdias.jose! We believe that this post does not fit the main topic of this site. Duplicate of previous question For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a re ...
written 25 days ago by Emily_Ensembl14k
4
votes
1
answer
124
views
1
answers
Answer: A: How to download an unspliced transcript for a given Ensembl ID using the perl AP
... There's no direct method for this. I would get the [transcript slice][1], then the [sequence of the slice][2]. print "unspliced: ", $transcript->slice->seq, "/n"; [1]: http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Feature.html#a47535eb7cdd09f4a76504dcb97325e ...
written 25 days ago by Emily_Ensembl14k
2
votes
1
answer
343
views
1
answers
Comment: C: can someone read this result to me
... I think the dominant/recessive thing is an oversimplification. Many genes are able to compensate if their opposite number is missing or broken, but not always. There may be haploinsufficiency, which is where a certain amount of protein is needed, and one copy of the gene is just not able to make eno ...
written 27 days ago by Emily_Ensembl14k
0
votes
1
answer
343
views
1
answers
Comment: C: can someone read this result to me
... I found the gene in Ensembl and looked at the [cDNA sequence][1]. I used the line numbering to find the appropriate position, and since it's not highlighted, that tells me that there's no variant at that locus in the database. [1]: http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db= ...
written 27 days ago by Emily_Ensembl14k

Latest awards to Emily_Ensembl

Scholar 12 days ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Scholar 13 days ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 19 days ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 25 days ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Commentator 27 days ago, created a comment with at least 3 up-votes. For C: How to write well in science, specially in bioinformatics ?
Scholar 5 weeks ago, created an answer that has been accepted. For A: misc_RNA in Ensembl
Scholar 5 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Where To Find A Dna For Trying Out My Analysis On?
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Where To Find A Dna For Trying Out My Analysis On?
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Where To Find A Dna For Trying Out My Analysis On?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: How to write well in science, specially in bioinformatics ?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Ensembl VEP 89 Output Format
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 7 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Where To Find A Dna For Trying Out My Analysis On?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Ensembl VEP 89 Output Format
Scholar 7 weeks ago, created an answer that has been accepted. For A: Ensembl VEP 89 Output Format
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: Do You Feel Good Or Bad About Putting Your Photo At Biostar?
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Making bioinformatics help and tutorials open
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Ensembl VEP 89 Output Format
Scholar 9 weeks ago, created an answer that has been accepted. For A: Ensembl VEP 89 Output Format

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1382 users visited in the last hour