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Ridom TraceEdit 1.1.0


Description of

Ridom TraceEdit


Edit DNA trace with this tool. Ridom TraceEdit is a cross-platform graphical DNA trace viewer and editor. TraceEdit displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format. Incorrect base calls can be edited and saved. TraceEdit is freely available and designed to operate on Windows, MacOS X and UNIX platforms.DNA sequencing has been the standard against which other types of DNA testing is compared. Major advances in DNA sequencing include the development of automated sequencers, discovery of fluorescent terminator chemistry, and cycle sequencing. These developments have made sequencing easier to perform and therefore more widely used. Currently, sequencing is used to identify microbial drug resistance mutations, cancer predisposition, somatic mutations, and genetic diseases. With the sequencing of the human genome and the "new era of molecular medicine", one can only expect the use of DNA sequencing to increase. Therefore, an increasing number of people need to check the evidence for individual DNA sequences by inspecting the chromatograms (more commonly known as trace files) from which the base calls were deduced. Trace files are stored in proprietary formats, such as those of ABI, or public formats such as SCF.Ridom TraceEdit can read ABI and SCF trace files and displays their contents. The software can be used to locate and delete the extent of low quality data at both ends of the sequence (trimming by Ns or low base quality values if available). It also enables the user to edit the base calls and to save them in SCF file format. A typical display from TraceEdit includes the name and additional information of the sequence being inspected, the menu bar, the file list pane with tool bar, and the trace editor pane with tool bar. In the file list pane a trace file can be chosen to be displayed in the editor pane. The trace editor pane shows the trace data, the quality values (if available), the original sequence, the edited sequence, and the base positions. The extent of poor quality data at the left of the reading is denoted by gray shading. A separate text window (not shown) is used to display the textual data contained in the file.Ridom TraceEdit Features:1. Operate on Windows, Mac OS X, and Linux operating systems2. View ABI and SCF chromatogram files3. Open at once several chromatogram files or whole directories4. Sort file list by different predefined options5. Navigate file list by keyboard shortcuts6. Scale the trace peak size vertically and horizontally7. Scroll a trace to a desired position8. Select bases from the trace9. Search for sequences using regular expressions10. Display or hide original base calls11. Display or hide quality values, if included in the chromatogram file12. Display as text other chromatogram information contained in the file13. Display as text the DNA sequence of your chromatogram14. Display the reverse complement of a trace15. Mark or unmark bases of interest (low quality, ambiguities)16. Import sequences from NCBI nucleotide database by accession numbers17. Print a trace18. Produce a PDF of a trace19. Copy, paste, and edit sequences20. Use contextual menus to copy, paste, and edit21. Trim sequence ends by Ns or low base quality values22. Save traces in SCF format23. Export base calls as a FASTA sequence24. Initiate a BLAST search from edited sequence25. Communicate directly from within the program with the developers for bug reports and feature requests26. Update the program automatically online


Published by: ridom.de
Downloads: 533
File Size: 5.8 MB
License: Freeware
Product Homepage: Visit ridom.de
Release Date: 31 December, 2012
OS: Windows
Download Location: Primary Download Link Broken? Report it!


Ridom TraceEdit 1.1.0 Download Tags:
RIDOM    StaphType    TraceEdit    TraceEditPro    QAlign    16S rDNA    SpaServer    Concise Guide to Mycobacteria    spa    protein A    MRSA    MLST    Assembler    assembling    DNA sequence    Editor    Software    Staphylococcus aureus    Typing    bacteria    mycobacteria    mycobacterium

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