Similar protocols

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 http://bio.lundberg.gu.se/edu/translat.html and compared to related sequences using the basic local alignment search tool (BLAST) at http://blast.ncbi.nlm.nih.gov/ Signal peptides from the deduced amino acid sequences were predicted by SignalP 3.0 (http://www.cbs.dtu.dk/services/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 (www.ch.emnet.org/software/TMPRED_form.html) and two-dimensional structures were designed by Protter Sever (http://wlab.ethz.ch/protter/start/)., 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