Question: Extract genes from gene list
0
gravatar for Bioblazer
2.2 years ago by
Bioblazer50
Pune
Bioblazer50 wrote:

I have list of genes from Aspergillus flavus fungi. From uniprot and Ensembl where I can able to retrieve the protein and CDS sequence respectively for my list of genes in multi-fasta format.But for gene sequence for each time I able to retrieve only one gene at a time. So is there any database where I can download whole set(total set) of gene sequence from gene list in a mutli-fasta format? Please suggest me.

Thanking you in advance.

sequencing sequence • 915 views
ADD COMMENTlink modified 2.2 years ago by genomax64k • written 2.2 years ago by Bioblazer50

Please, do provide a list of ten gene identifiers. It could help ;-)

ADD REPLYlink written 2.2 years ago by SamGG20
1
gravatar for genomax
2.2 years ago by
genomax64k
United States
genomax64k wrote:

If all you need is a list of gene sequences then you can get them from the Ensembl genome ftp page for A. flavus. You can then parse out the genes you need (if not all) from those files.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by genomax64k

Thank you for reply, If I am not wrong in ensembl whole genome download is possible but those sequence are available in scaffold level. But I need total gene sequence of an organism.

ADD REPLYlink written 2.2 years ago by Bioblazer50
0
gravatar for Pranavathiyani G
2.2 years ago by
Pondicherry, India
Pranavathiyani G220 wrote:

May be this might help - > Batch Entrez

ADD COMMENTlink written 2.2 years ago by Pranavathiyani G220

I tried but it did not work.

ADD REPLYlink written 2.2 years ago by Bioblazer50

Then you can try with E-utilities

Edit: Batch Entrez is working!

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Pranavathiyani G220

Thank you I will try with E-utilities and Batch entrez again

ADD REPLYlink written 2.2 years ago by Bioblazer50
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