Computational protocol: Comparative in vivo gene expression of the closely related bacteria Photorhabdus temperata and Xenorhabdus koppenhoeferi upon infection of the same insect host, Rhizotrogus majalis

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Protocol publication

[…] The samples were sequenced at the Biotechnology Center, Madison, WI, USA. These sequences were edited and assembled using Editseq (DNASTAR) and Contig (Vector NTI). Similar sequences were identified using BLAST algorithms (blastx and tblastx) in GenBank of National Center for Biotechnology Information and database of Xenorhabdus genomes (. The functions of identified sequences were assigned using Gene Ontology . The redundancy of each gene was counted cumulatively and the library coverage was calculated using Analytic Rarefaction ([] which has been used for estimation of total transcript diversity in the cDNA library [-]. […]

Pipeline specifications

Software tools BLASTX, TBLASTX
Application Nucleotide sequence alignment
Organisms Photorhabdus temperata, Caenorhabditis elegans
Diseases Nematode Infections
Chemicals Iron, Maltose