Calculate PSSM scores for E. coli promoters:

-10 box promoter:

How to use:
Input known σ70 -35 and -10 elements internal to a gene, these can predicted from existing tools if unknown.

Either 6 or 9 nucleotides must be input into either entry space, all sequences with the targeted codons must be included.
- A TGCTAT promoter element wholly within the codons for Cys/Tyr would be input as just the 6 nucleotides in the elements.
- A TGCTAT promoter element across three codons for Val/Ala/Ile (gtTGCTATt) would be input as the 9 nucleotide sequence corresponding to the three codons.

A sequence ranked by log odds score will be output for each sequence input.

For 6 nucleotide sequences, only the 6 input nucleotides will be treated as the promoter element and modified via CORPSE (Codon Restrained Promoter Silencing).
For 9 nucleotide sequences, a ranked table will be generated which iteratively treats each hexamer in the sequence as a potential promoter and targets those. All potential promoter sequences within the nonamer will be analysed and displayed.

*Amino acids reference table