I have lists of genes obtained from a differential expression analysis in tomato. I would like to use a tool to predict the % of differentially expressed genes having a predicted signal peptide to the chloroplast. I started with TargetP and ChloroP, however it is not possible to use long lists and it also need the full FASTA sequence of the gene. Is there any alternative using the gene ID as an input?
Thank you!
You can get most of the information from Uniprot. They run all their sequences through these predictors and then insert the annotations on the individual protein pages in section PTM/Processing. If you want a list of your proteins then go to Uniprot -> Retrieve/ID Mapping. There you can copy/paste your gene names or, better yet, uniprot IDs. Then you'll get a table of proteins. By clicking on Columns you can add column Signal peptide and then just download the whole table.
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