Other models based on observed sequence variability in large alignments of homologous protein sequences, such as the BLOSUM family [5], have proven popular and successful.
Based on observed sequence conservation/variation between Blumeria graminis, Sclerotinia sclerotiorum and Botrytis cinerea, PHYLORPH proposed 133 "Accepted" SCPCH for oak powdery mildews.
To map the two evident paralogs of C4-PPDK, we designed markers for each gene based on observed intronic sequence variation.
For each IS group, sequences obtained from PCR fragments were aligned with Bioedit, and pairwise nucleotide divergence between each pair of sequences was calculated with MEGA ver 4.0 based on observed nucleotide substitutions (sequence alignments are available upon request).
Here, we present the first computer program for classification of a given metagenome into chromosomal and plasmid sequences, based on observed differences in their pentamer frequencies.
Custom Perl scripts (available from http://awcmee.massey.ac.nz/downloads.htm) were used to simulate 35-bp reads at random positions in the sequence and to introduce errors in these reads based on observed error profiles from previous GA sequencing experiments.
In the GeneSV system, each proposed codon mutation is initially characterized using 9 criteria, which are based on observed similarities with corresponding positions in genomic and protein sequences from available databases.
The resistance level of a vPhenotype is based on observed phenotypic fold-changes (FC) in IC50 associated with the replication of a virus with a given sequence.
He distilled them into a mode of chaste abstraction based on observed fact: details of architecture, happenstances of light and shadow.
cRichness is based on observed unique OTUs.
