[ensembl-dev] GRCh37 Protein sequence has asterisks

[Luke Goodsell]

Thanks, Will,

Unfortunately, I cannot find cDNA from RefSeq – their sequences contain UTRs. Is there an easy way to identify the start and stop codons? The longest ORF is not always the correct one, unfortunately.

Incidentally, being able to get the sequences used by VEP is very important for us; we’re trying to construct the new protein sequences that result from variants using consequence information annotated by VEP. We’d very much appreciate the corrected sequences being incorporated into the otherfeatures database as soon as possible.

Kind regards,
Luke

From: William McLaren <wm2 at ebi.ac.uk>
Date: Tuesday, 5 December 2017 at 09:15
To: Luke Goodsell <l.goodsell at achillestx.com>, Ensembl developers list <dev at ensembl.org>, Alessandro Vullo <avullo at ebi.ac.uk>
Subject: Re: [ensembl-dev] GRCh37 Protein sequence has asterisks

Hi Luke,

There is no straightforward way to do this via Ensembl at the moment; I’d suggest you download the relevant files from NCBI.

The BAM files we use are obtained from ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens/GRCh37.p13_interim_annotation/; it seems there’s a protein and rna FASTA file in there which may have what you need.

Otherwise you may find what you need in the parent directory ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens. I’m not familiar with NCBI’s FASTA layout so you’d have to investigate yourself!

Regards

Will McLaren
Ensembl Variation



On 4 December 2017 at 5:55:38 pm, Luke Goodsell (l.goodsell at achillestx.com<mailto:l.goodsell at achillestx.com>) wrote:
Hi Allessandro,
Is there a way to extract the BAM-edited sequences? I'd simply like to get FASTA files of the RefSeq cDNA and proteins as used by VEP.
Kind regards,
Luke


From: Alessandro Vullo
Sent: Monday, 4 December, 17:44
Subject: Re: [ensembl-dev] GRCh37 Protein sequence has asterisks
To: Ensembl developers list, Luke Goodsell

Hi Luke, The problem is likely to depend on RefSeq differing from the reference. Are you using VEP and then retrieving the sequence as annotated by it? Quoting the relevant people (VEP): "VEP uses BAMs to correct RefSeqs that differ from the reference, and without those the API can give incorrect translations. This will hopefully be fixed in future when the SeqEdit objects that VEP creates from the BAMs are incorporated directly into the otherfeatures DB." Hope that helps, Alessandro
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