Batch Retrieval of Coding Sequences
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9.1 years ago
fire_water ▴ 80

Hello, I have a long list of human gene names (for example CFTR, ABCA1) and I want to retrieve the coding sequences for each gene. Does anyone know of a way to upload this list and retrieve the sequences in FASTA format?

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9.1 years ago
Manvendra Singh ★ 2.2k

You can get it out from Biomart. I think you want to get cDNA for gene, if you want to have isoforms sequences you can download gtf file from table browser export the knownGene as a GTF

grep -w 'CDS' in.gtf > out.gtf

Just get fasta sequence from gtf using bedops

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Thank you! How can I exclude isoforms?

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if you want to have one sequence per gene then you would need to have one isoform,

I would take the sequence from longest isoform .

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