find NBCI transcript with longest coding sequence for a list of human genes

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4.4 years ago

User6891 ▴ 330

Hi,

I have a list of 500 human gene symbols. For each of them I want to find the NCBI transcript with the longest coding sequence. How can I do this?

ncbi transcript cds • 789 views

ADD COMMENT • link 4.4 years ago by User6891 ▴ 330

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Take a look at MANE project that is a collaboration between NCBI/EBI.

ADD REPLY • link 4.4 years ago by GenoMax 147k

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Is it possible to identify unambiguously all the genes using these gene symbols in ncbi search? Perhaps, additional filters like " AND Homo sapiens[Primary Organism] AND refseq[filter]" may be necessary. If it is possible, you may easily download all the sequences for different transcripts and then identify longest ones with rentrez package in R, using entrez_search to get id's and then entrez_fetch with rettype argument set to "fasta".

ADD REPLY • link 4.4 years ago by Alex Nesmelov ▴ 200

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