Inconsistent alignment procedures in separate parts of the alignment could also influence the accurateness of the resulting phylogeny.
In this article, we will discuss a new strategy for the selection of optimum parameter settings for data alignment procedures in chromatographic sample profiling.
We run a NIP extraction alignment procedure as described in more detail in the following, which aims at identifying orthologous and nearby intron positions within the data set.
Homology assignment for the ribosomal data was carried out using (i) a 'progressive' alignment procedure as implemented in BlastAlign [43] for maximum likelihood (ML) searches using PHYML 2.4 [44], and (ii) a parsimony based sequence alignment applying the concept of dynamic homology [45], [46] in POY 3.0.11 [47], [47].
In addition, one may want to use automatically produced local alignments as anchor points to speed up the alignment procedure as outlined in [ 18].
These sequences, together with the nuclear, nucleomorph, plastid, and cyanobacterial sequences were aligned using the progressive alignment procedure implemented in CLUSTALX [ 29], edited to remove any ambiguously aligned regions, and conserved blocks of aligned residues (containing 495 amino acids) were used for phylogenetic analyses.
For peak alignment, only the (recommended) option of the "fast aligner" was tested as the other alignment procedure resulted in frequent crashes of the computer.
First, a new official gene set has been released since one of these studies, and second, the automated alignment procedure used in these studies would be unlikely to align ESTs to small genes (orphans are known to be small genes).
In the first case, we formulated a binding mode hypothesis for a series of 59 partial agonists at the human α 7 nicotinic receptor using an iterative unsupervised alignment procedure implemented in Open3DALIGN [2].
We therefore created a custom alignment procedure, written in perl.
In addition, we propose a force alignment procedure to correct for the drift in the experimental measure of the opening position, a major source of error.
