Each identity quartile shows similar representation within the group of 'correct' alignment boundaries (within ±10 residues of the embedded domain).
Aligned reads are grouped together and groups of overlapping alignments are defined as transcriptional units (TUs).
Each cell in the table is a box-whisker plot that displays the numerical scores (as quartile marks) produced by each [alignment method, scoring function] pair, over the five groups of (500) alignments each.
We then use the top-ranking group of BLAST-based alignments to annotate domains in the query sequence.
In this manner, a LTI can be paired with more than one group of non-overlapping alignments which could lead to several parent genes and hence several pseudogenes [ 16].
As in the pseudoreceptor model based on the Class I structures, in the model based on Class II structures (Figure 6B) Thr is placed as a hydrogen-bond donor in the vicinity of the esteratic or amidic group of the agonist alignment, and Tyr is placed near the middle electron deficient region.
Because the consensus shape is perfectly symmetric under all transformations in the symmetry group, the alignments of the transformed and relabelled copies of each configuration all share the same centroid and differ exactly by the symmetry transformations.
There is a similar relationship between the ratio of conserved/human-specific genes within each group of tissues and their alignment p-values, suggesting that alignment p-values are highly correlated with the conservation of tissue-selective genes and their corresponding pathways.
The following parameters were used for this search: "cross_match" as the search model; "slow search" to obtain a search 0-50-5%re sensithan then the standard; "fungi" to specify the species or group of input sequences and "alignment" to generate an output file showing the alignment.
The following parameters were used for this search: "RM_BLAST" as the search model; "slow search" to obtain a search 0-50-5%re sensithan then the standard search; "fungi" to specify the species or group of input sequences; and "alignment" to generate an output file showing the alignment.
Multiple sequence alignments of related proteins belonging to each group from both Arabidopsis and rice were performed using Multalin, which creates a multiple sequence alignment from a group of related sequences using progressive pairwise alignments (http://bioinfo.genotoul.fr/multalin/multalin).fr/multalin/multalin
