„  Information fields can be defined to contain “States”: predefined information categories. States can be assigned different colors to facilitate visualizing and mining database content. States can be defined as fixed content to avoid typing error and to restrict database entry to predefined choices.

„  The navigator can easily be removed by a menu item in the header

„  Less used buttons can be hidden

„  All panels in comparison window are now dockable

New alignment module

BioNumerics’ new interactive multiple alignment window combines an unparalleled number of features in one comprehensive window:

·            View normalized sequence trace files as in a contig assembler

·            Perform pairwise and multiple alignments using a variety of methods, including BioNumerics’ own algorithms optimized for speed and size, and ClustalW algorithms for perfection

·            Calculate rooted or unrooted trees using a variety of phylogenetic inference algorithms and display tree and branch confidence and significance values

·            Never lose control of sequence quality: displaying the curves for each base is just a mouse-click away – at any time, in any stage of the analysis!

·            Discover SNPs and mutations according to various parameters and criteria

·            Combine multiple genes in one single analysis and create global lists of SNPs and mutations

·            Drag the mouse to define a region of interest, and simply create a new analysis from it

·            Drag-and-drop manual realignment

·            True multistep undo/redo for manual editing and other functions

§   Perform and list multiple subsequence searches

§   Indicate regions of interest in a structured way using bookmark lists

§   Fully scriptable to add even more flexibility and to perform automated tasks in background

„  Combined view of aligned sequences, trace curves, phylogenetic tree, identity matrix, etc.:

„  Easy selection of genes or subsets from genes/samples. Each set or subset can be analyzed separately or results from searches such as SNP analysis can be combined:

„  Display nucleotide and/or amino acid sequences both in the alignment and the trace sequence viewer:

„  Choose between different alignment algorithms to optimize speed or accuracy:

„  Choose among a variety of tree inferring algorithms and calculate standard deviations, bootstrap values or cophenetic correlation of branches:

„  Perform searches for specific types of mutations, on selected or all alignments:

„  Display SNPs according to user-defined criteria, along with multiple alignments, dendrograms, nucleotide and amino acid sequences, trace files, consensus and sequence numbering. Perform SNP by SNP in-depth evaluations, with simple mouse clicks:

Band matching

„  Optimized visualization for matched and selected bands

„  Drag & drop changing of band class

Multiple alignment

„  Full transparency of sequence base changes in open comparisons and existing alignments

„  New nodes for e.g. user prompt and attachments

„  New Colored bar graphs in the chart & statistics tool

„  Resampling possible at import

„  Matching will be show even if the match got overruled manually

NEW: Batch Sequence Assembly plugin

With the Batch Sequence Assembly Plugin, you can import hundreds or thousands of sequence trace files in batch and assemble them automatically into contigs. The tool is very flexible and highly automated, offering the following main features:

·         Direct import of sequencer trace files from Applied Biosystems, Amersham and Beckman automated sequencers and supporting various other sequence formats.

·         Flexible file name parsing for (1) recognizing trace files belonging to same contig; (2) assigning sample ID information, and/or (3) linking imported sequences to existing database entries.

·         Optional import of sample and experiment information from tab-delimited text file.

·         Global and detailed reporting of warnings and errors encountered during assembly.

·         Recording and of warnings and errors per batch, per experiment and per sequence, with status “new”, “read” or “solved” and optional comments.

·         All import and assembly settings are saved and can be reused for next batches.

„  Select batch assembly reports per batch, per sequence type, or for any selection of database entries.

„  Display global reports for all sequences and detailed reports for all problems per sequence.

„  Double-click on a problem to pop up the Assembler with the problem position highlighted.

NEW: HIV Drug Resistance Analysis plugin

Based on decision networks, this tool is extremely powerful and flexible for up-to-date prediction of anti-retroviral drug therapies.

„  Evaluate resistance rules based on the known SNPs in the HIV pol gene, or create your own rules

„  Fully automated, designed for high-throughput reliable HIV drug prediction with flexible reporting possibilities