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I have been researching NCBI eutils and wish to get some 'big data' from it. I know that I can construct queries to query one of (I think) 8 databases, like this:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=nucleotide&id=2765657

which queries the nucleotide database for an id 2765657.

I am looking for a query that will return:

  1. genetics sequences.

  2. functional annotations of the sequences (e.g. exons, introns)

  3. metadata (e.g. chromosome)

Would anyone be able to show an example of how to search the eutils to get samples of records as described above?

I would need to know:

  1. Which database to search?
  2. how to list available records?
  3. how to query for a sample of the records?

Any help would be greatly appreciated.

Many thanks.

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  • $\begingroup$ The Entrez module in Biopython is able to do all the task written here. $\endgroup$
    – Shred
    Apr 8, 2019 at 14:02
  • $\begingroup$ thanks Shred, I am aware of this module - but have not tried it yet. Would it be able to help me in determining which database would be best and which filters would be useful? Many thanks $\endgroup$
    – Joey Gough
    Apr 8, 2019 at 14:42
  • $\begingroup$ I am looking for complete protein coding gene sequences, from one organism, preferably expressed in close temporal and spatial proximity, that have have quality annotations (e.g. exons, introns, codons). I have no particular preference on the model organism. Just looking for something to exercise LSTMs on. $\endgroup$
    – Joey Gough
    Apr 9, 2019 at 17:13
  • $\begingroup$ ok I got a gff3 file from GENCODE - this looks good $\endgroup$
    – Joey Gough
    Apr 9, 2019 at 17:33

1 Answer 1

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Downloading all this using an E-utils search would be cumbersome as you would have to search against multiple databases. For your specific needs, a GTF/GFF3 file would be good. Basically, a GTF/GFF file has genome annotations (positions of features) and includes features like exons, CDS and in some cases even special codons (such as that for selenocysteine). This file would not have the sequences but you can retrieve the sequences from the corresponding genome sequence fasta file using the co-ordinates described in the GTF file. There are several software tools that can do this; for example gffread and bedtools-getfasta (you can even write your own script which would not be very difficult).

You can download the GTF and the corresponding genome fasta files from these sources:

You should look at the details of the genome assembly. Different releases/sources may have different extents of curation.

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