Computational protocol: A Nematode Calreticulin, Rs-CRT, Is a Key Effector in Reproduction and Pathogenicity of Radopholus similis

Similar protocols

Protocol publication

[…] Sequence homology comparisons were conducted using the BLASTX and BLASTN programs from NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi). The ORF finder program was employed to predict the open reading frame (http://www.ncbi.nlm.nih.gov/gorf/gorf.html). The protein transmembrane regions, molecular weight, theoretical isoelectric point, glycosylation sites and hydrophobicity sites were predicted using the Protein Machine software available at ExPASy (http://www.expasy.ch/tools/). The signal peptide for secretion and the cleavage site were predicted using the SignalP 3.0 server []. The amino acid (aa) sequences of Rs-CRT (AFK76483) and six other CRT proteins from M. incognita (AAL40720), C. elegans (NP_504575), Necator americanus (CAA07254), D. destructor (ACV33082), B. xylophilus (ADD82420) and Pratylenchus goodeyi (AIW66697) were aligned using DNAMAN. Based on the aa sequences of 22 CRT proteins from 20 species, a neighbour-joining phylogenetic tree was constructed using MEGA5.0 []. […]

Pipeline specifications

Software tools BLASTX, BLASTN, Open Reading Frame Finder, SignalP, DNAMAN
Databases ExPASy
Application Phylogenetics
Organisms Solanum lycopersicum, Caenorhabditis elegans, Radopholus similis, Meloidogyne incognita
Diseases Nematode Infections, Parasitic Diseases