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Pipeline publication

[…] apore)., DNA sequences were evaluated using BioEdit V7.2.5. The edited sequences were translated to protein using web based translation software at and compared to related sequences using the basic local alignment search tool (BLAST) at Signal peptides from the deduced amino acid sequences were predicted by SignalP 3.0 ( Other divergent sequences were compared via multiple alignment using ClustalW in the BioEdit program. Transmembrane regions were predicted using the TMpred Server ( and two-dimensional structures were designed by Protter Sever (, Phylogenetic relationships among TSPs from a range of organisms were constructed based on amino acid sequences. ORFs were aligned using ClustalW. A phylogenetic tree was constructed with p-distance matrix using the neighbor-joining method with 1,000 bootstrap samplings in the MEGA software package version 6.0.6., The large extracellular loop (LEL) regions of Ov-TSP-2 (amino acid residues 109–185) and Ov-TSP-3 (amino acid residues 110–184) were obtained by PCR using plasmid containing the full length mRNA sequences of Ov-tsp-2 and tsp-3 (as described above) as templates. The primers for LEL of Ov-TSP-2 were: forward primer TSP2_ECF 5′-ACGCGAATTCCGCGATAAGATCCCCGG-3′, and reverse primer TSP2_ECR 5′-ACGCGCGGCCGCCTGGATGAACTCTTCGAC-3′; primers for LEL of Ov-TSP-3 were: forward primer; TSP3_ECF 5′ACGCGAATTCGACCATGTGAAAGAA-3′, and reverse primer; TSP3_ECR, 5′ACGCGCGGCCGCTTCGATGAATTTATC-3′, respectively. The fragments were integrated into the EcoRI and NotI sites (underli […]

Pipeline specifications

Software tools Protter, Clustal W, MEGA