Similar protocols

Pipeline publication

[…] equi and biovar ovis (Table ) were used in this study. Most of these genomes were sequenced by our group and are available at NCBI. We downloaded the genome sequences in gbk format from the NCBI server (ftp://ftp.ncbi.nih.gov/genomes/Bacteria) and the corresponding protein sequences (curated CDSs) were exported using Artemis Annotation Tool [] for further analyses., A high throughput biological workflow, MHOLline (http://www.mholline.lncc.br), was used to predict the modelome (complete set of protein 3D models for the whole proteome) for each Cp strain. MHOLline uses the program MODELLER [] for protein 3D structure prediction through comparative modeling. Furthermore, the workflow includes BLASTp (Basic Local Alignment Search Tool for Protein) [], HMMTOP (Prediction of transmembrane helices and topology of proteins) [], BATS (Blast Automatic Targeting for Structures), FILTERS, ECNGet (Get Enzyme Commission Number), MODELLER and PROCHECK [] programs. The protocol used here was modified accordingly from the original work by Capriles et al., 2010 []. Briefly, the input files of protein sequences were used in FASTA format for all strains because the MHOLline accepts only .faa format files for the whole process. Firstly, MHOLline selected the template structures available at the Protein data Bank (PDB) via BLASTp (version 2.2.18), using the default parameters (e-value ≤ 10e-5). Secondly, the program BATS refined the BLASTp search for templ […]

Pipeline specifications

Software tools BLASTP, BLASTN, HMMTOP