title: Genix: a new online automated pipeline for bacterial genome annotation.
abstract: Next-generation sequencing has significantly reduced the cost of genome-sequencing projects, resulting in an expressive increase in the availability of genomic data in public databases. The cheaper and easier is to sequence new genomes, the more accurate the annotation steps have to be to avoid both the loss of information and the accumulation of erroneous features that may affect the accuracy of further analysis. In the case of bacteria genomes, a range of web annotation software has been developed; however, many applications have yet to incorporate the steps required to improve their result, including the removal of false-positive/spurious and a more complete identification of non-coding features. We present Genix, a new web-based bacterial genome annotation pipeline. A comparison of the results generated by Genix for four reference genomes against those generated by other annotation tools indicated that our pipeline is able to provide results that are closer to the reference genome annotation, with a smaller amount of false-positive proteins and missing functional annotated proteins. Additionally, the metrics obtained by Genix were slightly better than those obtained by Prokka, a state-of-art standalone annotation system. Our results indicate that Genix is a useful tool that is able to provide a more refined result, and may be a user-friendly way to obtain high-quality results.
authors.affiliation: Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil, 96010-610 fred.s.kremer@gmail.com ls_pinto@hotmail.com.
authors.forename: Frederico Schmitt
authors.initials: FS
authors.lastname: Kremer
authors.affiliation: Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil, 96010-610.
authors.forename: Marcus Redü
authors.initials: MR
authors.lastname: Eslabão
authors.affiliation: Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil, 96010-610.
authors.forename: Odir Antônio
authors.initials: OA
authors.lastname: Dellagostin
authors.affiliation: Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil, 96010-610 fred.s.kremer@gmail.com ls_pinto@hotmail.com.
authors.forename: Luciano da Silva
authors.initials: LD
authors.lastname: Pinto
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D030541:Databases, Genetic; D001330:Electronic Data Processing / Q000379:methods; D048168:Escherichia coli K12 / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods; D016680:Genome, Bacterial / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D007921:Leptospira interrogans / Q000235:genetics*; D008089:Listeria monocytogenes / Q000235:genetics*; D058977:Molecular Sequence Annotation / Q000379:methods*; D009169:Mycobacterium tuberculosis / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins
keywords: genomics; next-generation sequencing; prokaryotes; webserver; whole-genome shotgun