This is a test version of Biostars. For the public version, visit https://www.biostars.org.
FASTA sequence retrieval

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

fasta genes degs
• 1,714 views • link
written by Roy.anupama11 • Roy.anupama11

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.

• 0 views • link
written by bioinfo_ga • bioinfo_ga

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)

• 0 views • link
written by Roy.anupama11 • Roy.anupama11

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

• 0 views • link
written by GenoMax GenoMax

1 answer

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

• 0 views • link
written by hello_bioinf • hello_bioinf

Log in to answer this question.

More posts like this