A phylogenetic tree was inferred from multiple sequence alignment of the amino acid sequence.
Phylogenetic trees were inferred from multiple alignments of protein sequences using appropriate programmes from the PHYLIP package, version 3.57c [ 40].
They were inferred from multiple alignments of homologous sequences using Rate4Site, which builds the phylogenetic tree using a neighbour-joining algorithm and estimates rates with an empirical Bayesian approach and the JTT model of sequence evolution [ 27, 28].
Tree topologies for gef (guanine nucleotide exchange factor), LacI (PurR/LacI family of bacterial transcription factors), pdz, ph, pii1 (a signal transduction protein), ptb, sh2, sh3 and GST (glutathione S-transferase) are inferred from multiple sequence alignments chosen from Pfam database (version 7.3).
Thus, potential roles of cysteine residues in regulatory disulfide bonds based on evolutionary conservation could not be inferred from a multiple sequence alignment.
But it can be inferred from (48 - 51 48 - 51for multhate SUs, the sub-carrier assignment and power allocation are not independent oforach other and the solution to the equations cannot be obtained directly.
The nature of the calls can also be inferred from the peaks (in multiples of 7 days) in the distribution of gaps (Figure 1(a)).
In addition, the recent introduction of RNAi libraries facilitates knock-down experiments in cell culture but the active RNAi sequence cannot be inferred from the sequence alone making multiple constructs necessary [ 4, 5].
As can be inferred from these various definitions, there are multiple levels of creativity definition, with a few recurring thematic concepts.
The confidence of sites mapped with PhosphOrtholog can be inferred from the "E-value" significance score (multiple testing corrected p-value; see Methods for details), obtained from the pairwise sequence alignments of orthologous proteins.
