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A web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. The predicted protein sequences can then be used as the input for additional annotation tools, such as InterProScan, for identifying protein families, domains and functional sites, the Conserved Domain Search service for the detection of structural and functional domains, and SignalP for locating potential signal peptides.


Combines Genewise with our own homology-based method, AlignFS, to identify protein-coding regions and correct erroneous frame-shifts, suitable for subsequent phylogenetic analysis. We compared AlignWise against other open reading frame finding software and demonstrate that the AlignFS algorithm is more accurate than Genewise at correcting frame-shifts within an order. We show that AlignWise provides the greatest accuracy at higher evolutionary distances, out-performing both AlignFS and Genewise individually. AlignWise produces a single ORF per transcript and identifies and corrects frame-shifts with high accuracy. It is therefore well suited for analysing novel transcriptome assemblies and EST sequences in the absence of a reference genome.


Simplifies the execution and data integration from heterogeneous biological sequence analysis tools. Pegasys enables the execution and integration of heterogeneous biological sequence analyses. It allows users to create workflows using any combination of the available programs in this program by dragging/dropping and linking graphical icons that represent sequence analysis tools. It can execute and integrate results from ab initio gene prediction, pair-wise and multiple sequence alignments, RNA gene detection and masking of repetitive sequences.