Difference between revisions of "DNA Baser"
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* Mark specific regions (like discrepancies, low-quality areas in chromatograms) with visible colors and quickly navigate to these regions | * 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...) | * Convert between different file formats (ABI, SCF, FASTA, multi-FASTA, GBK...) | ||
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Features proposed in v4 | Features proposed in v4 | ||
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* Blast automated searches and analysis of the results | * Blast automated searches and analysis of the results | ||
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| + | Automation | ||
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| + | 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. | ||
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| + | 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. | ||
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Revision as of 10:05, 10 September 2012
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Application data |
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| Created by | Heracle BioSoft SRL |
|---|---|
| Biological application domain(s) | Structural variation, SNP discovery |
| Principal bioinformatics method(s) | Assembly, 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. |
| Programming language(s) | Compiled |
| Software libraries | N/A |
| Licence | Trial/Shareware |
| Operating system(s) | Windows |
Summary: Tool for manual and automatic sequence assembly, analysis, editing, sample processing, metadata integration, file format conversion and mutation detection.
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Description
DNA Baser Assembler is unique bioinformatics software for manual and automatic DNA sequence assembly, DNA 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
- 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.
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 |
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