How to retrieve sequences of genes from TreeFam
How can I retrieve sequences of genes (not proteins) of some gene family from TreeFam database?
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yaroslav.sharov24 •
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yaroslav.sharov24 •
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Do you already have the protein sequences? If so, maybe you can use http://emboss.open-bio.org/rel/dev/apps/backtranseq.html to get the Nucleotide sequences.
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For your question, general instructions would be download the Mappings from TreeFam identifiers (Ensembl) to other databases (e.g. UniProt, RefSeq), check if this file has mapping to genes, then 1) if yes, use these IDs to download from the source (e.g., Ensembl BioMart); 2) if no, map the protein IDs to gene / transcript IDs and then download the sequences (BioMart is again one of the many options, see List of Ensembl Transcript IDs corresponding to protein-coding genes ).