Retrieve Gene Sequences Via Programming From Gene Databanks

Question

[hamed2005]

Hi dears!

I have a local database of miRNA::gene interactions for hsa, which contains just "GeneID" (Entrez ID) and "Gene Name" for Genes. I want to extract gene sequences for my genes either with the name or with the ID.

I have two different ideas:

1)I thought about finding a complete downloadable database of human genes, containing id,name and whole sequence of the genes! which I could not find!

or

2)using bioperl (or other similar stuff) and Bio::DB::EntrezGene to extract the gene sequences but it seems that "Bio::DB::EntrezGene" is broken : http://stackoverflow.com/questions/16199037/bioperl-module-biodbentrezgene-no-longer-working

what do you suggest dudes? I am really confused!!!

[Neilfws]

You can fetch sequences using Entrez ID as the filter in BioMart. Please search this site for the many usage examples.

[Hamish]

Please note there are many BioMart installations providing many different databases, in this case you mean the Ensembl BioMart, and most likely the "Ensembl Genes" database available from that BioMart, which contains annotations using Entrez Gene.

[hamed2005]

yeah bro! It was a semi-solution for me! just a question: which field in the "Ensembl BioMart" is related to the Gene Sequence? (there are lots there!)

[Neilfws]

When you click "Attributes", you should see "Sequences" as an option right at the top.

[hamed2005]

Tnx, yes I know, Im now working on BioMart . Do you mean using EMBL Perl API ? or something else?

Answer 1

[SRKR]

You can probably use links like there:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=fasta&retmode=text&id=**6701965,6701969,6702094,6702105,6702160**

Append the gene IDs or GI IDs or RefSeq IDs at the end separated by commas, a file is getting downloaded with all the sequences in FASTA format.

Source: FASTA Batch Download Using Entrez

Answer 2

[SRKR]

You can use this online tool to download fasta/genbank sequences from NCBI by submitting the GI IDs:

NCBI Sequence Retriever

Let me know if your requirement is different from what this tool provides.

[hamed2005]

tnx , but it needed gi ID which i don't have, (I have EntrezGene ID and Gene Name), besides there is no way to interact with it via Perl or etc, cause I have more than 1000 genes to be extracted, and it should be done just through programming! let me know about any other options!

P.S: by the way! your tools were cool! I visited your website and I really appreciate your works!