DNA Baser
|
Application data |
|
| Created by | Heracle BioSoft SRL |
|---|---|
| Biological application domain(s) | Structural variation, SNP detection |
| Principal bioinformatics method(s) | Sequence assembly, Sequence assembly editing, Sequence analysis |
| Technology | Sanger, 454 |
| Created at | Heracle BioSoft SRL |
| Maintained? | Yes |
| Input format(s) | ABI, FASTA, GenBank, SCF, SEQ, FASTA, TXT, CSV, 454 |
| Output format(s) | ABI, FASTA, GenBank, SCF, SEQ, FASTA, TXT |
| Software features | Portable. Does not require installation. Can run from USB stick. Only 3MB. |
| Software libraries | N/A |
| Licence | Commercial, Freeware |
| Operating system(s) | Windows |
Summary: Tool for manual and automatic sequence assembly, analysis, editing, sample processing, metadata integration, file format conversion and mutation detection.
"Error: no local variable "counter" was set." is not a number.
Description
DNA Baser Assembler is unique bioinformatics software for manual and automatic DNA sequence assembly, Nucleic acid sequence analysis, automatic sample processing, contig editing, metadata integration, file format conversion and mutation detection.
DNA Baser concentrates on automation of sequence assembly process. With DNA Baser Sequence Assembler, you can:
- Assemble multiple DNA samples or align to a reference sequence
- Batch assemble or align in groups of sequences by name
- Automatically clip sample ends (low quality region trimming)
- Automatically detect and trim recognition (vector/primer) sequences
- Import and analyze sequences from ABI, SCF, FASTA and SEQ
- Preview chromatograms with a single click
- View and edit sequence traces
- Mark specific regions (like discrepancies, low-quality areas in chromatograms) with visible colors and quickly navigate to these regions
- Convert between different file formats (ABI, SCF, FASTA, multi-FASTA, GBK...)
Features proposed in v4
- More accurate SNP detection
- Base caller
- Blast automated searches and analysis of the results
Automation
The proprietary assembly algorithm is optimized for accuracy and not for speed. This is needed in order to allow DNA Baser to automate the sequence assembly process. The program automatically removed the low quality ends, assemble the input samples, generates the contig/consensus then it automatically corrects the ambiguities. The data for ambiguity correction is obtain from the quality value assigned to each base in the input file. At the end the user-defined vectors are automatically removed from the contig and the metadata is added to the file. The contig is also automatically saved to disk as FASTA. The automation makes user's input unnecessary.
This allows DNA Baser to take the sequence assembly to the next level through a sophisticated batch assembly module in which thousands of contigs can be obtained in minutes instead of days. The user defines the folder where the input files are and a pattern. Based on this pattern, the program automatically detects sequences belonging to the same set/contig and assembles them together. The process described above is applied to each set. The contig is automatically saved to disk then the program moves to the next set with a speed of about one contig per second. The results of the process are written in a detailed log. The program highlights the assemblies that requires user input in red.
The graphic interface
The graphic interface is also optimized for speed and automation. For example, if the program was already set up from a previous session (the user settings are kept even after program restart) the user can assemble a set of files with only two clicks: the user drags and drops the files into the program then it pressed the 'Start assembly' button.
History
DNA Baser was first released in 2004. Since then it was constantly updated. The list of features is based on 'user request' which means that the end user can ask for new features and vote in a poll which features to be implemented first. DNA Baser was the first program to offer automatic end trimming, automatic vector removal and automatic sequence assembly (batch assembly).
Price
The cheapest option is to rent the software for one or six months. The price starts at $69. A 'for life' license is $499. The price is the same for all countries. The Academic licenses are about 20% cheaper than Business licenses. There are no additional fees (such as maintenance and support fees). The producer allows 'on spot' purchases: the license can be purchased online and the activation key is sent few minutes later via email. This allows the customer to use the software immediately. An 'affiliate' program is available. The affiliate receive up to 35% for each sale it makes.
Links
- DNA Baser Publication full text [ edit link ]
- DNA Baser Manual [ edit link ]
- DNA Baser Mailing list [ edit link ]
- DNA Baser Description [ edit link ]
- DNA Baser Binaries [ edit link ]
- DNA Baser HOWTO [ edit link ]
- DNA Baser Related [ edit link ]
References
none specified
To add a reference for DNA Baser, enter the PubMed ID in the field below and click 'Add'.
Search for "DNA Baser" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
