Question: How to get Fasta Sequences with their gene name for many genes?
2
gravatar for seta
4.9 years ago by
seta1.2k
Sweden
seta1.2k wrote:

Hi all,

I have a list of many gene name (about 5000) and I want to retrieve their corresponding fasta sequence. To this end, I try to use biomart, but it give me just nucleotide sequence. In fact, we cannot select more than one option in the "Attributes" part and we choose "sequence" in this part, so I cannot have their associated gene name for these sequences. Could you explain me how to have both nucleotide sequence and their related gene name. any suggestion would be highly appreciated.

sequence gene • 3.2k views
ADD COMMENTlink modified 4.9 years ago by Matt Shirley9.1k • written 4.9 years ago by seta1.2k
3
gravatar for Matt Shirley
4.9 years ago by
Matt Shirley9.1k
Cambridge, MA
Matt Shirley9.1k wrote:

I think this query is what you are looking for. You just need to select the gene name in the header information for the returned data file.

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Matt Shirley9.1k
2
gravatar for Manvendra Singh
4.9 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

you can have your gene in bed file (if not then download genes.gtf and convert it to genes.bed

first coloumn 'Chr' , second coloumn 'Start' third coloumn 'End' and then 'strand'

if you have whole genome fasta e.g. genome.fa

just use bedtools to extract fasta

getFastaFromBed -fi genome.fa -bed genes.bed -fo genes.fasta.out

details are here

http://bedtools.readthedocs.org/en/latest/content/tools/getfasta.html

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Manvendra Singh2.1k
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