Computational protocol: Genotyping of Chlamydophila psittaci using a new DNA microarray assay based on sequence analysis of ompA genes

Similar protocols

Protocol publication

[…] All available sequences of the ompA gene of C. psittaci were downloaded for analysis from the database of the National Center for Biotechnology Information (NCBI). A total of 210 sequence entries were found (by the date of manuscript submission). Of these, 89 sequences shorter than 500 nt were excluded from further analysis for failing to cover all four variable domains. Of the remaining 121 entries, 68 were found to belong to C. psittaci and 53 to other Chlamydophila species. Only 25 sequences from C. psittaci and 28 from other Chlamydophila spp. were found to include the full coding sequence (CDS) of approximately 1212 nt. In contrast, 70 entries lacked terminal parts of the CDS, but were retained because for some genotypes not a single complete sequence was available. All items were included in a global ompA sequence alignment using the program E-INS-I of the MAFFT package [].Classification was done first by visual inspection of the alignment using Clustal X [] and subsequently by calculating a sequence similarity matrix (see Additional file ), from which a split network graph was constructed (Fig. ) using the program SplitsTree4 [].Before starting the similarity matrix calculation, redundant items were removed, i.e. any sequence that could be retrieved under another sequence was deleted, and only unique sequences were kept. The sequences were brought to identical length by cropping highly conserved 3' ends in order to avoid distorted results due to alignment of differently sized sequences. Thus, the analyzed segment comprised 992 nucleotide positions (median sequence length 942 nt) including all four variable domains. The final set contained 63 unique sequences. […]

Pipeline specifications

Software tools MAFFT, Clustal W, SplitsTree
Application Phylogenetics
Organisms Chlamydia psittaci, Chlamydia abortus