Web services on MAMMOTH-mult server [40] were used to compute multiple structure alignments and additional pairwise structural alignments were made with SoFiSt program [72].
The influence of various atomic partial-charge formalisms, alignment schemes and additional molecular descriptors was evaluated in order to produce the highest quality models.
A companion website provides visualization of the EST alignments and splice graphs for each cluster showing alternative splicing, as well as access to the alignments themselves and additional information (see http://combi.cs.colostate.edu/as/chlamy/).edu/as/chlamy/
In a set of 246 alignments of CNEs between human, zebrafish, fugu and lamprey (Methods), we identified 61 conserved motifs, representing 22 fold enrichment over shuffled alignments (Methods and Additional File 3).
In the EamA MAFFT-EINSI alignment (see Methods and additional file 4: dmt.aln.tgz), 97.5% of the sequences have EamA in the first domain position.
For instance, our popular remote homology detection server, HHpred, now allows pairwise comparison of two sequences or alignments and offers additional profile HMMs for several model organisms and domain databases.
Using MP as optimality criterion 22 bipartitions are highly supported based on all six alignments, and an additional one based on five out of six alignments.
These non-coding transcripts were removed for adjusted transcript-to-protein alignments (Table 3 and additional file 1, Table S8).
Again, our multiple sequence alignment and phylogenetic analysis (Additional file 3) shows that the P. rapae lysozme is related to other lepidopteran lysozymes.
Our multiple sequence alignment and phylogenetic analysis (Additional file 2) shows that the P. rapae cecropins are virtually unrelated to worm cecropins, more closely related to other lepidopteran cecropins and distant from dipteran cecropin.
