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Exon inton structure

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.

intron exon
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updated by Ram Ram • written by rakeshmbb • rakeshmbb

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

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written by andrew.j.skelton73 andrew.j.skelton73

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

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written by rakeshmbb • 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.

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written by rakeshmbb • rakeshmbb

2 answers

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.

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updated by Ram Ram • written by andrew.j.skelton73 andrew.j.skelton73

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

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updated by Ram Ram • written by Antonio R. Franco Antonio R. Franco

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