Using Web Services To Get Fasta Files For Refseq Nm And Nr Identifiers

Question

[Laura]

I would like to be able to fetch fasta files for given refseq cdna or rna sequences programatically

I can do this for EMBL cdnas using a wget command like

wget  -q -O - "http://www.ebi.ac.uk/ena/data/view/BX648399.1&display=fasta" > BX648399.1.fasta

Does anyone know if there is an equivalent service at the NCBI

thanks

Answer 1

[Pierre Lindenbaum]

Use NCBI Efetch:

$ curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=BX648399&rettype=fasta&retmode=txt" | head
>gi|34367561|emb|BX648399.1| Homo sapiens mRNA; cDNA DKFZp686M11224 (from clone DKFZp686M11224)
GGCCACGGCCGACATGTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTAACACAATGGCCCTGCCTCCCACCGCTTTATTTCTTTCGGTTTCGG
ATGCAAAACAAAAAATTTTAAAAGAAAATGTGACTTCAAAGGAAAAGAACAAATTTCCAAAGACTTGGGG
GAGTGAAGGCAGAGCCTGGTGCAGATGGACGAGGTCTGCAGACGGAGGGCAGAGGTGGTGGAAGGGGCCA
GGGGCCTGCAGGCCTCCCCCTGGAACTGGGACTGGTCTCGGTCTGCTGACGTCAGGGTCAGCTCCCCCGC
GGAGCTGACTTCAGCAGCCCACAGCTGTGGGGCTTCAGCAGCCACACCAGCCCAGCCCAGCCCAGCTCTC
GATACGTTTGGTCTTTCATGCTGAAAAATAA

[Laura]

fantastic thanks

Answer 2

[Damian Kao]

Yes you can use eFetch: http://www.ncbi.nlm.nih.gov/books/NBK25498/#chapter3.ESearch__ESummaryEFetch