[EMBOSS] about 'helixturnhelix'e

[pmr at ebi.ac.uk]

Hi Jean,

> Now that I know the reason why patmatmotifs can't find HTH in my
> hair_drome
> input sequence, I would like to know what program in EMBOSS package CAN
> find
> it in my sequence. I tried helixturnhelix but still it couldn't find it.
> Does helixturnhelix using matrix or motif? looks like matrix to me in the
> documentation. Please advise.

helixturnhelix uses a matrix, but it is quite an old one from the days
when there were only about 20 HTH examples (and 2 of them were wrong).

We will look at ways to use the prosite matrix entries.

regards,

Peter