Computational protocol: Sequence analysis and phylogenetic study of some toxin proteins of snakes and related non toxin proteins of chordates

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Protocol publication

[…] Protein sequences of cytotoxins, short neurotoxins and related non-toxin body proteins were retrieved from National Centre for Biotechnology Information (http://ncbi/nlm/nih.gov) []. Presence of signal peptide within the amino acid sequences and cleavage sites of signal peptides was analyzed using SignalP 4.0 algorithm which is a neural network-based method (http://www.cbs.dtu.dk/services/SignalP/) []. Main chain of protein sequences were selected for further analysis. For simplicity a sequence ID code was given to each molecule. Sequence related information's was mined from Protein Information Resources (PIR) knowledgebase []. Multiple sequence alignment is done with Clustal-X program, followed by manual inspection for errors []. Aligned sequence sets were represented in Clustal-X coloring scheme and polarity coloring scheme using Clustal-X and Jalview tool respectively [, ].Sequence logos were generated using WebLogo application, which helps to dictate the sequence conservation and relative frequencies of the amino acid residues at each position [, ]. Family specific conserved pattern of amino acid residues in toxin and non-toxin proteins were extracted using PRATT version 2.1 []. Phylogenetic trees were re-constructed using neighbor-joining method implemented in MEGA 4.0 version []. For Bayesian inference of phylogeny, MrBayes 3.1.2 was used []. […]

Pipeline specifications

Software tools SignalP, Clustal W, Jalview, WebLogo, MEGA, MrBayes
Applications Phylogenetics, Genome data visualization
Diseases Neurotoxicity Syndromes