In the next step, the initially obtained 1,634 candidate contigs were split into batches of 150 sequences and each batch was also added to the master alignment using MAFFT (-add option) resulting in 11 separate alignments.
To accomplish this, separate alignments are aligned together while preserving the columns in the individual alignments.
A small number of reads (20,835) were defined as chimeric by the mapping software and had two separate alignments included in the output, which in the vast majority of cases were situated on different chromosomes.
gambiae H1 candidate proteins (XP_311486) to a histone H1 protein from C. thummi, and examined the alignment for precise matches (Fig. 1A) that did not match well in a separate alignment of the An.
Evolutionary divergence was estimated in separate pairwise alignments for different functional domains of the OPRM1 gene (Ks, Ka, Ku for exons and Ki for introns) for closely related rodent (mouse and rat) and primate (human and macaca) species, and for distantly related species (human and mouse).
Therefore we employed an alignment procedure that uses a linear Hidden Markov Model (HMM) as implemented in the software SAM (Sequence Alignment and Modelling system) [ 84] for separate alignments of the three data sets.
The separate alignment option aligns all sequences against different references separately in a run.
In addition to the full protein alignments, we built a separate alignment for PDZ domains (as in ref [ 2] but with an extended gene sampling) and constructed specific alignments for the SAM and SH3 domains of Shank.
The overall alignment of the six AAA protomers in midasin from human, yeast and Giardia was created by first making separate alignment of the three organisms for each of the six AAA protomers.
A separate alignment was then edited manually for each allele.
