COLOMBO is a software framework equipped with a GUI for the prediction of genomic islands (GIs) in prokaryotes. It can be equipped with different plugins that actually perform the prediction. The current version of COLOMBO is supplied with SIGI-HMM that uses hidden Markov models and codon usage bias; SIGi-CRF utilizing conditional random fields and tetramer-based order-3 Markov chain transition probabilities. In particular, SIGI-CRF analyzes non-annotated genomic sequences. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-142 SIGI_CRF-AUTO SIGI_CRF-AUTO is an alternative front-end to the SIGI-CRF processing core. First, it allows to batch process a large number of genome sequences and/or to run a variety of parameter combinations. Second, it can collect all individual prediction results generated by varying parameter combinations and combine them into a single graphical representation. Once rendered, images can be saved very flexible with a broad variety of format options.
