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Virtual protein merger
Allows users to determine putative open reading frames based on tandem mass spectrometry (MS/MS) ion search results of a virtual protein database. Virtual protein merger is a software that considers peptides associated to a virtual protein in a same translation frame. Then, the program computes the probable position of the corresponding open reading frame by searching for flanking start and end codons while authorizing users to define a minimum threshold score for accepting a peptide match.
Open Reading Frame Finder
Searches open reading frames (ORFs) in the DNA sequence. Open Reading Frame Finder returns the range of each ORF, along with its protein translation. It uses ORF finder to search newly sequenced DNA for potential protein encoding segments, verify predicted protein using newly developed SMART BLAST or regular BLASTP. This web version of the ORF finder is limited to the subrange of the query sequence up to 50 kb long, but the stand-alone version, doesn't have query sequence length limitation.
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