Ncbi Direct To Obtain Gene And Exon-Only Sequences

Question

[g]

Hi,

Is there an automated way to take the human genome and make a table with all the genes on a sequence (exons+introns) with indices placed in separate columns. And then to make another file with all the exon regions with indices in separate columns.

I thought NCBI Direct would be easy to make this possible but seems harder than I thought.

Thanks, Nuc

Answer 1

[t.c.a.smith]

Try Ensembl Biomart. http://www.ensembl.org/biomart/martview/ I know it allows you to get this information at the chromosome level.

From "CHOOSE DATABASE" select Ensembl Genes 75. From "CHOOSE DATASET" select Homo Sapiens Genes. Under "Filters" on the left hand menu expand "Region" and the select your chromosome. Under "Attributes" on the left hand select "Structures" and from here you can select various gene and exon indices for the chromosome for export. for export click results in the top left and then decide on you export format.

you could also query this programatically using perl, although i have not done this myself, there are most certainly questions on BioStars relating to this.

n.b. I believe the Ensembl annotations are more liberal than the the NCBI so they may include genes or exons that NCBI do not.