EMBOSS Plugin Program List
The EMBOSS Tools are added to the Sequence menu within Geneious Pro. Descriptions courtesy of the EMBOSS website.
Predict Antigenic Regions (antigenic) – Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. (Sequence -> Locate Features menu)
Back Translate (backtranambig) – Takes a protein sequence and makes the nucleic acid sequence it could have come from. It does this by generating nucleotide ambiguity codes that represent all possible codons for each amino acid. (Sequence menu)
Protein Charge Graph (charge) – Plots a graph of the charges of the amino acids within a window of specified length as the window is moved along the sequence. (Graph in Sequence View)
Predict Secondary Structure (garnier) – An implementation of the original Garnier Osguthorpe Robson algorithm (GOR I) for predicting protein secondary structure. (Sequence -> Locate Features menu)
Mutate Sequence (msbar) – Changes a sequence a lot or a little, attempting to emulate various forms of mutation. You can set the number and types of mutations. (Sequence menu)
Search for PROSITE Motif (patmatdb) – Searches for a PROSITE style motif within a group of protein sequences and annotates any matches. (Sequence -> Locate Features menu)
Shuffle Sequence (shuffleseq) – Takes a sequence as input and outputs one or more sequences whose order has been randomly shuffled. No bases or residues are changed, only their order. (Sequence menu)
Predict Signal Cleavage (sigcleave) – Predicts the site of cleavage between a signal sequence and the mature exported protein. (Sequence -> Locate Features menu)
Fickett Testcode Graph (tcode) – Plots a graph of the Fickett Testcode statistic that predicts if a specified window of DNA is protein-coding or non-coding. (Graph in Sequence View)
Search for Transcription Factors (tfscan) – Takes a DNA sequence and the name of of a taxonomic group and does a search for matches against binding sites in the TRANSFAC SITE database. (Sequence -> Locate Features menu)