User: Andy Yates

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Andy Yates110
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Ensembl Core Software Project Leader

Posts by Andy Yates

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Is Zlib Library Failing To Process Properly Bgzip Files?
... Hi. I have just encountered the same problem and it seems there is a pure-Perl solution surrounding this as shown below my $status = gunzip("in.gz" => "out.gz", MultiStream => 1) or die "gunzip failed: $GunzipError\n"; It also seems Apache Commons Compress can provide similar support for ...
written 2.6 years ago by Andy Yates110
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Comment: C: How To Get All Ensembl Repeatfeatures From Biomart Or The Ensembl Rest Api?
... Also you can switch the output to JSON using the following URL http://beta.rest.ensembl.org/feature/region/human/3:1000-200000.json?feature=repeat ...
written 4.4 years ago by Andy Yates110
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Answer: A: Map The Protein Sequences Of Unknown Genes That Have Uniprot Names To Ensembl Ge
... Hi, As the person who works very closely with Ensembl's xref system. Ensembl's UniProt xrefs come from two sources. The first is direct association where a UniProt annotator has made an assertion about the link between us & them. The second is an alignment using Exonerate. I haven't investigate ...
written 4.5 years ago by Andy Yates110
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Answer: A: Help Interfacing With Ucsc Annotations Using Mysql
... Hi there Have you considered using Ensembl's variant effect predictor? You can find more information from here http://www.ensembl.org/info/docs/variation/vep/index.html. However just for reference you can submit upto 750 snps to our website interface, you can download the script and run it locally ...
written 4.6 years ago by Andy Yates110
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Answer: A: Displaying Information Regarding The Quality Of The Ensembl Genomes
... Hi, It is important to differentiate the production and provision of genomes. Ensembl distributes INSDC genomes and then attempts to annotate; we do not produce genomes. INSDC do store a lot of this information so we try to provide links back to INSDC via assembly accessions, location in the core m ...
written 5.1 years ago by Andy Yates110
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Answer: A: A Quick Way To Match A List With Ensembl Gene Ids To The Specific Ensembl Db Ver
... Hi John, Firstly the REST API does not support previous versions and is something we are currently discussing how best to support archive versions. Once we come up with a way to do this we will let everyone know. Secondly you can do this lookup using the latest Ensembl DB since we retain all stabl ...
written 5.1 years ago by Andy Yates110
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Comment: C: Mapping Uniprot To Ensembl Genes
... So as far as my knowledge of all of these things go Ensembl maps its proteins to UniProtKB accessions using a 100% identity match (please assume this even though data in 67 will disagree) or by using a direct association given to Ensembl by UniProt. The BioMart referred to in this post is the Ensemb ...
written 5.4 years ago by Andy Yates110
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Comment: C: Mapping Uniprot To Ensembl Genes
... Just to add another link into this mix from the Ensembl interface; http://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000204970;r=5:140165876-140391929;t=ENST00000378133 . ...
written 5.4 years ago by Andy Yates110
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Answer: A: Mapping Uniprot To Ensembl Genes
... UniParc is another way of doing this mapping since this is based on checksum collisions from numerous protein resources. If you want a 1:1 mapping this is a good place to look. http://www.uniprot.org/uniparc/UPI00001273C7 ...
written 5.4 years ago by Andy Yates110

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