Computational protocol: Molecular Cloning, Expression Profile and 5′ Regulatory Region Analysis of Two Chemosensory Protein Genes from the Diamondback Moth, Plutella xylostella

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Protocol publication

[…] Amino acid sequences of CSPs (n = 27) were retrieved from an NCBI protein search using the keywords “chemosensory protein” and “lepidopteran”. Molecular mass and isoelectric point was predicted using the software, ExPASy (http://www.expasy.ch/). Multiple sequence alignment was carried out with the online service at http://bioinfo.genotoul.fr/multalin/multalin.html (). Promoter prediction and characterization were carried out using the Neural Network Promoter Prediction (NNPP) server (http://www.fruitfly.org/seq_tools/promoter.html) (). Sequence analysis seeking transcriptional regulation response elements was carried out with TFSEARCH (http://www.cbrc.jp/research/db/TFSEARCH.html) (). The signal peptide was predicted using SignalP 3.0 () at http://www.cbs.dtu.dk/services/SignalP-3.0/. The phylogenetic tree was constructed using MEGA 3.0 software () using the neighbour joining method, and it was reconstructed with 1000-replicate bootstrap analysis. […]

Pipeline specifications

Software tools MultAlin, NNPP, TFSearch, SignalP, MEGA
Databases NCBI Protein ExPASy
Applications Genome annotation, Phylogenetics
Organisms Plutella xylostella