We also discerned those markers uniquely aligned to A, B and C genomes, and those markers with multiple alignments to different genomes, respectively, which were used for the population genetic analysis for the diverse lines of the three A genome-carrying species.
Otterlace contains several modules: Zmap for a graphical view of the analysis and annotation data; Blixem and Dotter for viewing multiple and pairwise sequence alignments, respectively; and Lace for building and modifying transcript models.
Based on the multiple alignments, Ser450 and Lys415 were replaced by cysteines respectively, using the MutanBEST kit (TaKaRa Biotechnology, Dalian, China).
Additional files 11, 12 and 13 show multiple alignments of the vertebrate Syt2, Syt5 and Syt8 protein sequences, respectively.
We submitted the same multiple alignments having a length of 100 nt, 200 nt and 300 nt, respectively to each of the four web servers.
Multiple alignments of 255 and 322 nt of the N and F genes, respectively, were made by using the ClustalW program (www.ebi.ac.uk/clustalw).ac.uk/clustalw
Multiple alignments of these repeat domains together with one representative peptide of their corresponding homolog, respectively, further addressed their homology relationships (Fig. 2C and D).
Sequence information, genomic distribution, gene structure and multiple alignments of polypeptide were presented in Additional file 2, Figures 1, 2 and 3 respectively.
ClustalW multiple alignments revealed that the lancelet UCP-like sequence was 53%, 55% and 56% identical to sea bass UCP1, UCP2 and UCP3, respectively.
