GreenAcres analyses the DNA sequences of individual BAC clones and their contigs performing a combined automatic and manual approach. ORFs are predicted by versions of GENSCAN, GeneMark and Fgenesh. The programs are locally trained for moncot and dicot species as well as Orders such as Fabales, Cucurbitales and Brassicacales.

The quality of the ORF-predictions is displayed in Cluster Regions with overlap scores for the data. The Cluster Regions are mined for specific sequence context such as Transcription Start Site evaluation (TSSP), Polymerase II recognition sequences (N-SCAN), for C(p)G islands (CPGFinder) and strong plant motif searches (Nsite). Orthologous searches are performed in Gene Index databases for relevant similarities to Tentative Consensus sequences.

For all ORFs identified from the above described approach an exhaustive automatic bioinformatic analysis in respect to function and structure of the respective protein is performed using CLC Protein Workbench software. Annotation of description and functional categories will be according to the Gene Onthology (GO) classification system and Enzyme Commission (EC) numbers.

Repeat sequences and transposable elements will be identified using RepeatScout, RepeatMasker and BLAST in transposon databases.

The resulting database consists of fully integrated ORF and Gene Prediction and Annotation files and can be viewed and adapted according to the clients’ needs.