With the Sequence Types module, the user can assemble sequence reads ranging from single genes obtained on classical automated sequencers to full chromosomes on next generation sequencers. In addition, BioNumerics recognizes widely used sequence file formats such as EMBL, GenBank, and Fasta, and stores the full header and feature information of annotated sequences.
Starting from the Sequence Types module, BioNumerics provides a rich and uniquely integrated sequence analysis platform, offering a variety of analysis tools such as multiple alignment, phylogenetic clustering, chromosome comparison and alignment, automated annotation, chromosome-wide SNP analysis, primer design and discriminatory primer design, restriction enzyme analysis, frame analysis, etc.
BioNumerics' powerful database backend supports sequence analysis in high-throughput projects and the available plugins, script tools and pipeline engines allow for reliable automated batch-processing of massive amounts of sequence data.
Chromatogram-based sequence assembly
BioNumerics’ sequence assembler tool allows direct import of raw chromatogram files from automated sequencers. The assembler combines a powerful alignment engine with an informative and intuitive 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.
Power Assembler
The new Power Assembler is designed for preprocessing and assembly of Next Generation sequencer (NGS) data. The Power Assembler contains powerful algorithms for both mapped assembly using one or multiple reference sequences (resequencing) and de novo sequencing to assemble contigs up to full genome size from millions of reads. Power Assembler accepts data from Roche/454, Solexa/Illumina and FASTA or FASTQ files (Applied Biosystems SOLiD). With Power Assembler, the user can build pipelines that contain a specific series of steps (“actions”) in the preprocessing and template-assisted assembly of large sequencing projects.
Typical actions include:
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Loading reads (+ quality info).
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Loading reference sequence(s).
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Demultiplexing.
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Paired end splitting.
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Trimming and filtering of reads according to various quality criteria.
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Calculating global statistics on the project.
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Aligning the reads against the reference sequence(s).
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Exporting the sequence(s) to the BioNumerics database.
Through the availability of a large number of predefined "actions", the user can easily set up a basic assembly project pipeline. However, more experienced users can break down each action into its atomic "operators", and edit the pipeline at the deepest level or construct custom actions. The degree of flexibility with which workflows can thus be generated is practically unlimited. Action pipelines can be saved as templates and shared among users.
The interface is fully graphical with surveyable flowcharts for pipelines and actions and allows detailed reports, graphs and statistics to be calculated for each component. The Summary graphs resulting from specific actions (e.g. quality trimming, coverage histogram) allow parameters such as minimum read quality and read length to be set directly on the histogram.
Action pipelines can be saved as templates which can be used for automated high-throughput preprocessing and analysis. Depending on the type of project, pipelines can be tuned to run fully automatically, with all parameters predefined, or can request user input at specific steps. Pipeline templates can be modified and saved into new templates if requested.
Power Assembler projects can be opened from any other sequence analysis windows in BioNumerics, including the sequence editor, the comparison window, the multiple alignment window, the chromosome comparison window, etc. The viewport in the Power Assembler is automatically adjusted to the selected base in the analysis window so that doubtful bases or important SNPs can easily be verified from the source.
In combination with the Chromosome comparison tools (version 6.1) and the Annotation tools (6.5, see below), the Power Assembler renders BioNumerics into a powerful and integrated chromosome analysis platform.
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
