Inspection of amino acid sequence profiles suggests a division of the class III adenylyl cyclases in to four subclasses, class IIIa IIId.
The nematode specific sequence profiles from each orthologous group were aligned to the corresponding reference sequence profiles using CLUSTALW[42].
Zhou & Zhou used sequence profiles obtained not from CPD, but from structural alignment of small protein fragments, in combination with traditional sequence profiles.
This is because of the time dependent nature of sequence database for sequence profiles.
Other various physico-chemical sequence profiles were raised with in house software.
In order to compare two sequences, sequence profiles are built for both of them.
The input features of ANGLOR include sequence profiles, predicted secondary structure and solvent accessibility.
For facilitating the comparison within SP methods, we used original sequence profiles from Ref. [11].
The sequence profiles for queries were built based on the first step of the PDB-BLAST runs.
Sequence profiles i.e. Position-Specific Scoring Matrices (PSSM) were generated for all protein chains, using the iterative PsiBLAST program [37].
All the extracted local sequence profiles will be input into Prodepth along with other global sequence features.
