Exon inton structure

Question

[rakeshmbb]

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.

[andrew.j.skelton73]

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

[rakeshmbb]

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

[rakeshmbb]

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.

Answer 1

[andrew.j.skelton73]

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.

Answer 2

[Antonio R. Franco]

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