Which sequence is the one I am interested in?

Question

[zizigolu]

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

[Jean-Karim Heriche]

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.

[zizigolu]

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

[zizigolu]

Simply, the answer is the same as stated by Emily. Using biomart I retrieved the sequences without doubts

Answer 1

[Jean-Karim Heriche]

EnsEMBL's BioMart can export these: Attributes > Sequences > cDNA sequences

[zizigolu]

Thank you but there were just cDNA start and end and when I downloaded the result, there was just the the IDs name again

[Emily]

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.

Like so.

[zizigolu]

Thanks Emily