Getting out the protein translation

You have three approaches for getting out protein translations

• -pep available on all programs, provides the translations moving over frameshifts and introns
• -trans available on genewise/genewisedb provides the translations across introns but breaks on frameshift errors. This means that the translations can be correctly placed on the genomic DNA provided

• -mul available only on estwisedb when a HMM is used, provides a protein multiple alignment of all the DNA hits derived against the HMM match