motif detection from predicted gene models

Question

[Kay]

I've got a genome sequence (in scaffolds), in fasta format, RNA-seq bam files, predicted gene models from Braker and Augustus, I was wondering how to predict motifs. How can I detect motifs, say in the highly expressed genes? I have been reading about MEME, Hommer, etc, does it matter if my genome is from parasites, not humans?

Do I have to use Chip-Seq data?

Thanks K

Answer 1

[Carambakaracho]

Hi Kay,

there's many options, depending on the kind of motifs you're looking for

• hmmer with pfam or interpro
• low complexity with Dustmasker or tantan
• Protein motifs options in the EMBOSS package (also some for nucleic motifs)
• annotation via eggnogs
• etc.

All of these tools should support non model organisms, though a bit caution is always required

[Kay]

thanks Carambakaracho, I will have a look, my concern is genes predicted braker or Augustus lack promoter/enhancer/silencer regions, these tools prict genes from the start codons till stop codons