Genix: About

The tool

Genix is an online automated pipeline for bacterial genome annotation. The program takes a FASTA file containing a set of sequences, that can be complete chromosomes, contigs or scaffolds, and a tax_id identifier. First, a dataset of proteins associated to the tax_id "Is downloaded from Uniprot and used to build a raw dataset, wich may contain several redundances. CD-HIT (Li & Godzik 2006) is used to build a non-redundant dataset, wich is used to generate the final BLASTp (Altschul et al. 1990; Camacho et al. 2009) database. For the genome annotation, genix uses a combination of several bioinformatics tools, including Prodigal (Hyatt et al. 2010), BLASTp, tRNAscan-SE (Lowe & Eddy 1997), RNAmmer (Lagesen et al. 2007), Aragorn (Laslett 2004), HMMER (Eddy 2011), BLASTn and INFERNAL (Nawrocki et al. 2009), RFam (Griffiths-Jones et al. 2003), Antifam (Eberhardt et al. 2012) and the non-redundant dataset generated by CD-HIT. At the end, genix generates a genbank file, containing all the features identified for each sequence, and, if requested by the user, a the genbank submission file (.sqn) generated by tbl2asn.