Can you specify your gene_ID and what needs to be transformed. Generally, we can build a hash table from the annotation files to accomplish the transformation. For instance, {AT2G010110: TCP}.

Thank you for your message.

My gene_ID like this：augustus_masked-HiC_scaffold_1-processed-gene-1003.12. The transformation that I need is to convert the gene_IDs to their corresponding gene names,so I can choose them easily for further research.

I appreciate your suggestion of building a hash table from the annotation files to accomplish the transformation. This seems like a useful approach. But my annotation file doesn't exist the symbol column. Do you mean to create a new column to pick the gene name from the annotation column? Like pick the "stearoy-l ACP desaturase" from "gi|684183365|gb|AIN52151.1| stearoy-l ACP desaturase [Camellia oleifera]"?

Thank you again for your help.

One way is to use a bioinformatic tool called a "gene ontology (GO) annotator". Another way to get gene symbols after transcriptome data is to use a database of gene annotations.

Some of the most popular GO annotators are DAVID GoRILLA, and Panther.

Dayu Yang

If you need to extract information from a sequence identifier such as 'gi|684183365|gb|AIN52151.1| stearoy-l ACP desaturase [Camellia oleifera]', you can simply split the string using the '|' character and choose the last element of the resulting array. if the last element is different with your **gene_Name**, you can use a regular expression to match greedily