Question: Exon inton structure
0
gravatar for rakeshmbb
4.8 years ago by
rakeshmbb0
India
rakeshmbb0 wrote:

Hi...I am new in bioinformatics. I have nearly 100 protein sequence and the genome file of the organism. I want to know intron exon structure of every genes encoding the proteins. Please kindly tell me how can I do it.

myposts • 1.3k views
ADD COMMENTlink modified 4.6 years ago • written 4.8 years ago by rakeshmbb0

Do you have a list of the genes associated with the proteins, or IDs for the protein sequences?

ADD REPLYlink written 4.8 years ago by andrew.j.skelton736.0k

Hi.. I have ID of individual protein as well as the protein sequence....I have also the genome file in fasta format...

ADD REPLYlink written 4.8 years ago by rakeshmbb0

Hi....I have .gff file. It has all the genes of the organism. How can I retrieve information of only the genes I need. I can then use it in GSDS.

ADD REPLYlink written 4.6 years ago by rakeshmbb0
1
gravatar for andrew.j.skelton73
4.8 years ago by
London
andrew.j.skelton736.0k wrote:

Depending on what IDs you have for the proteins, you can use biomaRt in R to map up the IDs to gene ID's. You can then look up the gene IDs on the Ensembl track viewer and see the intron exon structure.

ADD COMMENTlink modified 7 months ago by RamRS27k • written 4.8 years ago by andrew.j.skelton736.0k
0
gravatar for Antonio R. Franco
4.8 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

Look for either a gff or gft file of your organism, because it has the information you are asking.

They are plain text files containing that information, so it will be easy to handle

ADD COMMENTlink modified 7 months ago by RamRS27k • written 4.8 years ago by Antonio R. Franco4.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1303 users visited in the last hour