I am working on finding lncRNAs and ncPEPs. I have used nf-core rna-seq pipeline for generating .GTF files. Then i filtered .GTF file to obtain transripts which are not annoted. Further i implemented CPC2 (Coding Potential Calaulator) standalone tool for separating coding and non-coding RNAs. Then i removed transcripts less than 200 nucleotides and used LncDC https://www.nature.com/articles/s41598-022-22082-7 tool for extracting LncRNAs. I have list of LncRNAs from LncDC. I am running a task for BLAST my ncRNAs against uniprotKB database to filter known.

How can I further filter these LncRNAs so i can find noval if there are any. Basically i want to check if these LncRNas are predicted before or not.

Also, my aim is to predict small non-coding RNA encoded peptides (ncPEPs).