The interaction contributions that determine the alignment of helical peptides in lipid membranes were analysed using model sequences, and peptides that change their topology in a pH-dependent manner have been designed.
Each sequence was successively fixed as a "family model sequence" and LEON produced an output list of "non-homologous sequences".
Sequences were assembled using the Staden package [ 46] together with the reference ORF model sequence and checked for differences.
Contigs for each of the Heterobasidion species were aligned with H. irregulare gene model sequences and between species.
Briefly, in a given cluster, each sequence is successively fixed as a "family model sequence" and tested against all other family members using LEON.
ProQM uses two sets of features, one that only depends on the model sequence and one that is calculated from the structural model.
The sequences obtained were compared with deposited sequence information using the BLAST algorithm (http://blast.ncbi.nlm.nih.gov/Blast.cgi/) excluding human and model sequences and restricting the displayed results to fungal sequences.
We matched RNAseq and array data based on the comparison of array probe and transcript model sequences and omitted those probes from further analysis for which no match was found.
Firstly, as the gene model sequences and the translated proteins derived from them are submitted to the public databases, they will appear authoritative, unless the investigator is familiar with the issues and chooses to look at the EST data.
So as to be able to model sequences and position them on a temporal axis, we used a set of predefined relationships according to a linear approach which includes the notion of the time lapse [ 27, 28].
