What are the tools used to annotate or predict functional elements (promoters, protein-coding genes, silencers, telomeres, splice sites etc.) in biological data?
From my research on the tools that are available for annotating functional elements, I found out that there are myriad of options. For instance, you can use MEME to find novel motifs (MEME - Submission form). In addition, GimmeMotif is another way to find motifs including transcription factor. You can read more details on the GimmeMotif on GitHub - vanheeringen-lab/gimmemotifs: Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples.