With the Sequence Types module, the user can analyze sequences of nucleic acids and amino acids. BioNumerics recognizes widely used sequence file formats such as EMBL, GenBank, and Fasta, and stores the full header and feature information of annotated sequences. In addition, BioNumerics’ powerful sequence assembler tool allows direct import of raw chromatogram files from automated sequencers. The assembler has both an excellent alignment engine and a smart, user-friendly interface.
The program allows for automated batch-processing in high-throughput sequencing projects such as for typing and surveillance. Complete gene assembly projects with aligned chromatograms can be saved into projects and popped up with a single mouse-click on a sequence stored in the BioNumerics database. Each sequence type in BioNumerics can be stored with its own reference sequence, and with specific alignment and clustering settings.
Sequence viewer
The sequence viewer stores sequences in rich format including all features and annotations known by EMBL and GenBank formats. This convenient window contains a number of tabs for different views and analysis applications (see also Molecular Analysis Tools module) and offers a number of unique features:
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Storing and handling sequences of up to full chromosome size.
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Displaying coding sequences, amino acids and any other features on annotated sequences.
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Displaying and editing contig assembly and trace chromatograms directly in the sequence editor.
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Creating additional information fields to describe sequences.
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Creating multiple subsequence searches and displaying all hits with their position, direction, mismatches, occurrence on graphical sequence viewer, etc.
Multiple sequence alignment
In combination with the Tree and Network Inference module, BioNumerics offers probably the finest and most comprehensive sequence alignment and clustering tools that currently exist for PCs. It combines clustering of thousands of nucleotide or protein sequences of almost unlimited length with multiple alignment and display of homology matrices. The versatile user interface allows sequences in multiple alignments to be displayed as raw chromatogram files as well as translated protein sequences, and direct editing is possible in any visualization. Multiple alignments associated with dendrograms can be edited manually in drag-and-drop mode, and a multistep undo/redo function makes editing even more convenient. In addition to well-established alignment algorithms described in the literature, the software contains extremely fast and reliable algorithms elaborated at Applied Maths.
SNP analysis
BioNumerics’ sequence alignment application is an invaluable tool for SNP and mutation analysis. SNPs or mutations are screened for through up to many thousands of aligned sequences and the software statistically calculates the probability of each SNP based upon the quality of the base assignments and the curves in the chromatogram files. Various filters allow for screening SNPs with specific thresholds or other features such as the type of mutation they induce. By looking at sequencer chromatograms directly, the user has excellent control over the probability of each potential SNP locus. Complete alignments, including all SNP and subsequence search listings, can be saved and re-edited at any time. Additional sequences can be added to existing projects.
The software offers a wide range of phylogenetic clustering techniques and various tools for the estimation of the significance and reliability of clusters, which are discussed in the Tree and Nerwork Inference module.
Bioanalysis made easy
