Hello everyone! I'm looking for bioinformatics tools to predict promoter regions in some Pseudomonas putida sequences that I have. Does anyone know of any software or online tools that could be useful for this?
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BPROM (Softberry) is the standard free tool for sigma70 bacterial promoters, and bTSSfinder if you want other sigma classes covered. Both are trained on E. coli though, so on P. putida treat the output as a hint rather than a prediction - Pseudomonads have a fairly different sigma repertoire.
If you already know which genes you care about, searching the upstream regions for the -35/-10 consensus directly (TTGACA, ~17 bp spacer, TATAAT, allowing a couple of mismatches) often tells you more than a predictor does, since you can see what the evidence actually is. Disclosure, I work on SeqBench: https://seqbench.com/tools/motif-finder does IUPAC codes with both-strand scanning and mismatches. Any pattern searcher does the same job.
And if you have RNA-seq for your strain, the 5' coverage step is better evidence than any of the above.
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For Pseudomonas putida, it's best to use multiple promoter prediction tools, as most are trained on E. coli and may produce false positives for Pseudomonas.
Some useful free tools are:
Also, check the Pseudomonas Genome Database for annotated TSS, operons, and regulatory information if your strain is available. If you have RNA-seq or TSS data, use it to validate predictions, as experimental evidence is much more reliable than sequence-based prediction alone.
Using a combination of BPROM/bTSSfinder + BacPP + Operon-mapper + MEME Suite usually provides a more reliable workflow than relying on a single tool.