DNASIS® MAX for DNA sequence analysis.

DNASIS® MAX is bioinformatics software which features a high degree of flexiblility, allowing users to add homology search, multiple alignment, and sequence linking functionality(Phred/Phrap) to an existing base set of intuitive and refined features for sequence editing / fundamental analysis.

New Features in Version

Equipped with a Sequence Input Wizard Navigates the capture of sequences when DNASIS® MAX is launched. Supports creating new sequences, inputting sequences from existing files, and search/reading in of files for sequence databases, and NCBI Entrez search/reading in of files.

Additional Site Search Functions Search for hair pin loops, tandem repeats, and stacking sites against entered DNA and RNA sequences.

Improved Functionality of the Analysis Button In versions up to V2.0, for setting analysis parameters, the analysis button needed to be right-clicked and a context menu chosen. In V2.2, when the analysis button is clicked, the dialog shown below will appear, and the analysis parameters may be set more easily. The dialog may be suppressed for analysis buttons that do not need to have many parameters altered.

Analysis Results List Display Button A button dedicated to displaying analysis results has been newly added. With this button, a consistent function allows for list display across analysis types and search types, such as ORF search, restriction enzyme search and motif search.

Parameter Set Button
Many analysis functions now include a button from the analysis parameter settings screen for restoring parameter settings to default values.

EMBL, PIR Formats Corresponding to the Features Key
The Features Key entries noted in EMBL and PIR formats may be analyzed and graphically displayed as annotations, similar to reading in with the existing GenBank file Features Key.

Opening Specific Entries from Multiple Entry Files
When opening a single file with multiple entries included, each entry to open may be specified individually. Up to 100 total entries may be opened in one window.

Stronger Sequence Database Functionality
1.Newly Added Search, Delete, and Renew Functions For the Sequence Database created by users, text searches on Entry IDs and Definitions are now supported. Also, entry deletions and renewals are also now possible.
2.Export to DNASIS® MAX FunctionThe searched sequence may be exported to DNASIS® MAX itself for conducting further analysis.

Main Features of DNASIS® MAX

Simple Operations: Conduct Analysis with One Button All analysis functions are conducted with buttons; simply click appropriate button to conduct analysis. Analysis results and sequences are integrated so that more intuitive operations can be used to conduct analysis. For example, a serial process such as translating an open reading frame and analyzing the hydrophilic and hydrophobic characteristics of its amino acid sequence, may be easily conducted.

Refined Graphical Display
Analysis results are displayed below the sequence, making the display easier to understand; while viewing analysis results, you can also edit other sequences easily. If multiple analyses have been conducted, each analysis result is added on to the display, so multiple results may be compared for a comprehensive evaluation of search results. Moreover, the Map display allows you to view with one glance the entirety of sequence and analysis results, even for analysis results of lengthy sequences. Particular areas of interest may be magnified for display, so moving to edit locations is also easy.

Simultaneous Etiting of Multiple Sequences
Multiple sequences may be edited simultaneously in one screen. Analysis results for multiple sequences may also be displayed on one screen. Also, multiple sequence alignments may be displayed and edited.

Support for Numerous File Formats
The following various formats may be automatically recognized and opened.

GenBank Format	Multi GenBank Format	Fasta Format
Multi Fasta Format	PIR Format	Multi PIR Format
EMBL Format	Multi EMBL Format	ABI Format
SCF Format	Text Format	OLD DNASIS Format

After editing, a specified range or the sequence itself may be exported in fasta, simple text, formatted text or MSF formats. All sequences displayed in the window may be saved in multiple files, or in a single file, in a single process.

Annotation Editor Feature The FEATURES table data in the GenBank format file may be automatically extracted for graphical display and editing. Moreover, users may add their own unique annotation data. For example, a myriad of analysis results, including searched ORF ranges, set primer positions and protein hydrophilic ranges may be saved as annotations. Multiple annotations, such as excised regions, maybe selected and joined together to comprise a new single sequence.

Drawing Plasmid Maps Plasmid maps may be drawn; restriction enzyme cut locations and annotations may be added, and standard shapes such as labels and arrows and double spirals may also be included in drawings.. Moreover, the restriction enzyme site search results atop the sequence editor and annotation editor contents may be captured to draw a plasmid map automatically. One or two desired restriction enzyme cutter points may be specified for DNA insertion.

Adding Comments
Comments may be added to sequences and each analysis result. If files in GenBank, PIR, EMBL, or fasta formats are opened, annotation data will be automatically captured.

Project
The contents displayed in windows such as multiple sequences, annotations and analysis results may be saved in one file as a project. This convenient feature allows for reexamining Blast searches and other analysis processes that take a long time without repeating the analysis, for sharing analysis results with project members, and for temporarily saving multiple sequences of interest.

Entrez Keyword Search
The Entrez system, offered through the NCBI Web site, is supported. Complex search conditions may be entered easily using a dedicated input screen. Sequences (or multiple sequences) specified from the keyword search results may be automatically downloaded from NCBI for edit/analysis.

Trace Display of DNA Auto-Sequencer Trace files in ABI and SCF formats may be displayed, so bases may be deleted or modified while looking at traces. Also, multiple traces may be displayed simultaneously. Displaying opposite strands of trace data is also possible. An alignment is conducted on the referenced sequence and the trace and alignment are displayed next to each other, which is effective for SNP extraction. Delete vector sequences prior for more convenient alignment.