FASTA sequence retrieval

Question

[Roy.anupama11]

Hi, I have got DEGs from reference based mapping and need to know the functional annotation of each one of them. How to do it? How to retrieve the fasta seq for a list of genes?

Thanks in advance

[bioinfo_ga]

You can make a bed file of the list of genes based on chr-start and end positions and then use Bed to Fasta to get the gene sequences.

[Roy.anupama11]

I tried doing the same but got the following error-

terminate called after throwing an instance of 'std::invalid_argument' what(): stoll Aborted (core dumped)

[GenoMax]

need to know the functional annotation of each one of them. How to do it? How to retrieve the fasta seq for a list of genes?

You are asking for two different things. Retrieving fasta sequence is not going to tell you anything about the functional annotation. You may get a bit more info if you retrieved GenBank/GenPept format, but in any case for functional annotation you may need to look elsewhere. e.g. GO annotation

Answer 1

[amy__]

Uniprot, KEGG pathway analysis, EGGNOG - there's quite a lot of tools and websites available that will tell you the likely function of a gene - this is just what I think of when I read your question, there may be better answers out there