ChloroP 1.1: changes from the previous version
The output format has changed as follows:
- the predicted cTP length is presented instead of the predicted cleavage
- the potential cTP length is presented for all sequences, even
if no presequence was predicted to be there (to provide maximum information
in borderline cases);
- the "detailed output" earlier available (and mandatory...) only when
submitting a single sequence is now optional for all types of submissions.
Multiple sequences may now also be input by "cut-and-paste" (use
3. The first 20 characters of sequence names will be preserved
throughout the prediction and presented on the ChloroP prediction result page
(as compared to 11 in previous versions. Wow! Great improvement, isn't it?).
1. Presentation of cleavage site score for every residue in a submitted
Presented only if only a single sequence was submitted. The cleavage site score
(calculated from a scoring matrix) is defined so that the predicted cleavage
site is located directly N-terminal of the highest score in a 40 amino acids
long stretch around the peak value of the network output score derivative.
Thus, there might exist one or several CS-score(s) that happen(s) to be greater
than the score of the proposed cleavage site, but since they are all located
outside the area comprising the 40 residues determined by the derivative, the
presented cleavage site is still what ChloroP considers as the most likely
site. The user may however feel free to search for other potential cleavage
sites; the cleavage site score was included in the output in order to make such
a search possible.
2. Length restriction on predicted transit peptides
To avoid prediction of absurdly long transit peptides, the cleavage site (or
rather the highest derivative) is searched among the 100 N-terminal residues.
In our set of 75 cTP-containing proteins, the longest cTP is 91 amino acids.
The restriction focuses the prediction on the N-terminal part of the sequences
while still allowing for smaller errors in the N-terminal part of the submitted