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Question: Tool to download fasta for accession id list
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gravatar for david.hughes
12 months ago by
david.hughes • 0
david.hughes • 0 wrote:

I have list of accession ids: eg. ABD26882.1, ABF53376.1, ABG05503.1. What Galaxy tool should I use to download nucleotide fasta from ENA or elsewhere?

download fasta bacterial protein ena • 416 views
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modified 12 months ago by Jennifer Hillman Jackson ♦ 25k • written 12 months ago by david.hughes • 0
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gravatar for Jennifer Hillman Jackson
12 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool Get Data > UCSC Archaea would be the best way. The Table Browser at that site will accept a list of accessions and send fasta sequence directly to Galaxy. This will only work if the bacterial genome is included there and a track containing the protein sequences exists - so you will need to check.

If the data is not at the UCSC Archaea browser, there are two other choices I can think of:

  • Go to ENA or NCBI directly, retrieve the sequences using their tools/methods, and upload the results to Galaxy after.
  • Use Get Data > EBI SRA. Retrieval will be one sequence at a time. The fasta results can be concatenated within Galaxy after. This will be a tedious method and should probably only be considered as a last resort for your use case (which is not a common query to run on Galaxy).

Thanks! Jen, Galaxy team
ADD COMMENT • link written 12 months ago by Jennifer Hillman Jackson ♦ 25k
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