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Search: Posts Made By: Giulietta
Forum: Bioinformatics 12-10-2013, 12:53 AM
Replies: 13
Views: 9,003
Posted By Giulietta
Hi sp144, Just to clarify, in the Ensembl...

Hi sp144,

Just to clarify, in the Ensembl pipeline Kcnq1ot1 has been annotated from RFAM, which has four separate entries:

RF01946 KCNQ1OT1_1 KCNQ1 overlapping transcript 1 conserved region 1 ...
Forum: Bioinformatics 12-05-2013, 01:42 AM
Replies: 13
Views: 9,003
Posted By Giulietta
I find Kcnq1ot1 in mouse on the forward strand,...

I find Kcnq1ot1 in mouse on the forward strand, consisting of a single exon:
...
Forum: Bioinformatics 02-25-2011, 04:37 AM
Replies: 3
Views: 3,595
Posted By Giulietta
You can find the Ensembl assembly for different...

You can find the Ensembl assembly for different versions in the species (human) home page:

http://www.ensembl.org/Homo_sapiens/Info/Index

The current assembly in Ensembl is GRCh37, which is...
Forum: Bioinformatics 02-25-2011, 04:27 AM
Replies: 9
Views: 4,315
Posted By Giulietta
Just a word about the Ensembl variant effect...

Just a word about the Ensembl variant effect predictor- if you have chromosome and base pair positions (on the reference assembly), you can enter in any alleles found at that position as your input. ...
Forum: Bioinformatics 01-14-2011, 06:26 AM
Replies: 6
Views: 4,612
Posted By Giulietta
If your bacteria is in EnsemblGenomes, you can...

If your bacteria is in EnsemblGenomes, you can use the variant effect predictor to calculate the effect of sequence variations on an Ensembl transcript (including any amino acid change). Start with...
Forum: Bioinformatics 01-05-2011, 06:06 AM
Replies: 12
Views: 9,901
Posted By Giulietta
Sorry about the broken link- we will endeavor to...

Sorry about the broken link- we will endeavor to fix it.

The link at www.ensembl.org is working:

http://www.ensembl.org/info/website/upload/var.html

Try to change uswest to www (and go back...
Forum: Bioinformatics 01-05-2011, 02:16 AM
Replies: 4
Views: 2,183
Posted By Giulietta
The pilot was done using NCBI36 (hg18). All the...

The pilot was done using NCBI36 (hg18). All the other annotation is on GRCh37 (hg19). These are indeed the standard assemblies.

http://browser.1000genomes.org/Homo_sapiens/Info/Index
...
Forum: Bioinformatics 01-05-2011, 01:46 AM
Replies: 12
Views: 9,901
Posted By Giulietta
Ensembl's variant effect predictor may be of use,...

Ensembl's variant effect predictor may be of use, here. If you enter in a genomic position and allele(s) it will let you know the position in the cDNA and the protein (if there is one) and the amino...
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