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motif detection from predicted gene models

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

motif rna-seq
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updated by Carambakaracho Carambakaracho • written by Kay • Kay

1 answer

Hi Kay,

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

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

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written by Carambakaracho Carambakaracho

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

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written by Kay • Kay

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