Refseq Mrna To Cds Sequence
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9.5 years ago
Woa ★ 2.8k

I've a long list of RefSeq mRNA Ids for a particular organism. I wish to download all the corresponding coding sequences(CDS) in fasta format, where available. Is their any suitable tool or script for automatically doing this?

Thanks in advance

WoA

refseq cds • 6.4k views
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Which organism?

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Mouse(Mus Musculus)

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4
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9.5 years ago
  • Go to the table browser http://genome.ucsc.edu/cgi-bin/hgTables
  • select group "Gene", track "RefSeq", table "refGene"
  • click "identfiers: paste list" and copy+paste your list
  • output format: CDS fasta
  • get output
  • Formatting options: unselect everything but "Show nucleotides"
  • get output
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9.5 years ago
Neilfws 49k

Normally I would suggest BioMart for this purpose (assuming that your organism is in BioMart) but as I write, it is giving an error. However, here's the procedure for when they fix it:

  1. Select MARTVIEW in the top menu
  2. Choose database Ensembl genes 64, select dataset for your organism
  3. Click Filters, left menu; expand "Gene"; check "ID list limit"; select "Refseq mRNA IDs"
  4. Paste or upload IDs
  5. Click Attributes, left menu; select "Sequences"; expand "SEQUENCES"; select "Coding sequence"
  6. Click "Results", top-left menu.

Currently, this gives the error "Serious Error: Error during query execution: Table 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist" - I will report this to BioMart.

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Message from Ensembl: "This is a known bug in BioMart for release 64. See the known bugs page here: http://www.ensembl.info/contact-us/known-bugs/. This bug will be fixed for release 65 due out in November."

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9.5 years ago
brentp 23k

If you're willing to try an in-development library, you can try cruzdb. With a script like this:

from cruzdb import Genome
db = Genome('hg19')

refGene = db.refGene

for name in (n.strip() for n in open("names.txt")):
    gene = refGene.filter_by(name=name).one()
    print ">%s" % name
    print "".join(gene.cds_sequence)

and names.txt containing id's like: NM_001127388 NM_001127389

It will create print FASTA file by querying the UCSC genomes database (refGene table), and grabbing sequence from their DAS sequence server.

If you have a long list, see the notes on the cruzdb page about mirroring the MySQL pages locally.

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Thanks I'll try that

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