Two new plugins for Geneious Pro: Vector NTI import and EMBOSS integration
Posted on 04 Mar 2008 20:25
Due to popular demand, EMBOSS tools and Vector NTI file importers have been added to Geneious.
EMBOSS Tools
The EMBOSS package is a popular set of tools used for analysis of molecular data in biology. The Geneious EMBOSS Tools plugin will initially include seven of these tools, with more to come in the future. The plugin currently features the following tools:
- Predict Antigenic Regions (antigenic) — Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar[1].
- 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.
- Predict Secondary Structure (garnier) — An implementation of the original Garnier Osguthorpe Robson algorithm (GOR I) for predicting protein secondary structure.
- 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.
- Search for PROSITE Motif (patmatdb) — Searches for a PROSITE style motif within a group of protein sequences and annotates any matches.
- 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.
- Predict Signal Cleavage (sigcleave) — Predicts the site of cleavage between a signal sequence and the mature exported protein.
Vector NTI Importer
The Vector NTI importer plugin allows users to import file formats created by Vector NTI. These include sequences (*.gb and *.gp file types), alignments (*.apr file type) and molecule, oligo and citation archives (*.ma4, *.pa4, *.oa4 and *.ca6 file types). Users can now easily import their Vector NTI files and run analyses on their data using Geneious.
From Geneious 3.6 the Vector NTI importer plugin will be bundled with Geneious and also include an enzyme archive (*.ea4 file type) importer. Both the Vector NTI importer plugin and the EMBOSS Tools plugin are freely available to Geneious Pro users from the Geneious plugins page.
References:
1. Kolaskar,AS and Tongaonkar,PC (1990). A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Letters 276: 172-174.
