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Pipeline publication

[…] often generates global alignments instead of local alignments with gap regions. We on the other hand maintained the integrity of exons preceding and following these gaps, and added alignment gaps accordingly. In case newly added myosins contained species-specific extended loops we adjusted the entire full myosin alignment accordingly. Similarly, divergent sequence regions were re-aligned as soon as further related sequence data became available (Additional file : Text). The final myosin motor domain alignment used in this study contains 3490 alignment positions and is available at Figshare., To exclude that our manually generated alignment leads to biased phylogenetic trees, we generated a MAFFT alignment (13,907 alignment positions), which results in similar trees (Additional file : Text). However, the MAFFT alignment contains only a few alignment blocks longer than 5 aa precluding its use in correcting gene predictions and in supporting gene structure comparisons., Protein domains were predicted using HMMER3 [] against the Pfam v.28.0 database [] accepting all domains with E > 0.001. Transmembrane helices were predicted with TMHMM v.2 [], single α-helices (SAH) with Waggawagga [], coiled-coil regions with coils [], and sequence motifs with PROSITE []. Domain ranges were corrected and domains manually added to the myosin schemes shown in Fig. , if additional domains were predicted in orthologous myosins and if these domains were supported by homology in the multiple sequence alignment. Domains, or parts of domains, could have been missed because of the applied E-value cut-off, or because they had not been identified at all. The latter happens if sequences are too divergent with respect to the Pfam domain profiles, which are generated based on seed alignments of small sets of supposed representative domain family […]

Pipeline specifications

Software tools MAFFT, HMMER, TMHMM