Recent changes

ChloroP 1.1: changes from the previous version

1. The output format has changed as follows:
  • the predicted cTP length is presented instead of the predicted cleavage site;

  • 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.
2. Multiple sequences may now also be input by "cut-and-paste" (use FASTA format).

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?).

Earlier changes

1. Presentation of cleavage site score for every residue in a submitted sequence

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 sequences.


Scientific problems:        Technical problems: