Which sequence is the one I am interested in?
Hey guys,
I was searching rRNA_gene sequence in Saccharomyces cerevisiae, in BioMart I found the Ensembl IDs.
In NCBI-nucletotide I typed one of the IDs, for example RDN18-2, but I found many hits there. From where could I select the one I am searching for please?
Thanks
• 2,085 views
•
link
updated
by
Jean-Karim Heriche
•
written
by
zizigolu
•
written
by
zizigolu
1 answer
EnsEMBL's BioMart can export these: Attributes > Sequences > cDNA sequences
• 0 views
•
link
written
by
Jean-Karim Heriche
At the top of the attributes page you should see six options with radio buttons:
- Features
- Structures
- Homologs
- Variation (Germline)
- Variation (Somatic)
- Sequences
Select sequences. You will get two sections to expand, Sequences and Header information. Choose cDNA from Sequences then add all the information you need in the Header.
Log in to answer this question.
More posts like this
-
gene ID conversion
written by Adishi •
-
Find and Download GenBank File for Whole Genome using Entrez
written by kmyers2 •
-
NCBI Saccharomyces cerevisiae GENE_INFO has child taxon ID instead of parent.
written by mbelmadani
-
removed entrie sequence include specific letters
written by Jason •
-
getting fasta sequence of a list of ensemble gene IDs
written by zizigolu
-
list of gene or transcript IDs and their length
written by zizigolu
-
ribosomal RNA for cleaning contamination during ribo-seq
written by zizigolu
-
getting the whole of rRNA.fa for ecoli
written by zizigolu
-
Determining the 5'UTR of Saccharomyces cerevisiae?
written by dashdp123 •
-
Why does biomart return multiple Entrez IDs
written by hdy
What's wrong with the sequences you got from EnsEMBL ? Why do you then need to go to NCBI ? Entering RDN18-2 in the search bar of the NCBI website would give you all sequences that contain this gene, e.g. the chromosome where it's on, any contig where it's been annotated.
Thank you, I need the fasta file (nucleotide) to make a reference fasta containing whole of yeast rRNA_gene sequence to remove the contamination from my ribi-seq data sets. Anyway I need the nucleotides not just IDs
Simply, the answer is the same as stated by Emily. Using biomart I retrieved the sequences without doubts