DNA sequence assembly (Gap4/Gap5), editing and analysis tools
DescriptionStaden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin). Gap4 performs sequence assembly, contig ordering based on read pair data, contig joining based on sequence comparisons, assembly checking, repeat searching, experiment suggestion, read pair analysis and contig editing. It has graphical views of contigs, templates, readings and traces which all scroll in register. Contig editor searches and experiment suggestion routines use confidence values to calculate the confidence of the consensus sequence and hence identify only places requiring visual trace inspection or extra data. The result is extremely rapid finishing and a consensus of known accuracy. Pregap4 provides a graphical user interface to set up the processing required to prepare trace data for assembly or analysis, and automates these processes. Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and ZTR trace files. Prefinish analyses partially completed sequence assemblies and suggests the most efficient set of experiments to help finish the project. Tracediff and hetscan automatically locate mutations by comparing trace data against reference traces. They annotate the mutations found ready for viewing in gap4. Spin analyses nucleotide sequences to find genes, restriction sites, motifs, etc. It can perform translations, find open reading frames, count codons, etc. Many results are presented graphically and a sliding sequence window is linked to the graphics cursor. Spin also compares pairs of sequences in many ways. It has very rapid dot matrix analysis, global and local alignment algorithms, plus a sliding sequence window linked to the graphical plots. It can compare nucleic acid against nucleic acid, protein against protein, and protein against nucleic acid.
11835 other people were interested in this package here. The newest known version of this software is 2.0.0+b11-4+b1 (Information last updated 1 day ago.)
Upload new screenshots
Thanks for uploading more screenshots. Please note:
- Your screenshot should contain a typical scene when working with it.
- Take only a screenshot of the respective application and not of your whole desktop (unless the screenshot is meant for a window manager).
- Your screenshots must be in PNG format.
- You can upload multiple images at once.
- Your screenshot need to be approved by the moderators first. You will already see your screenshot but it will not be visible to others instantly. If moderators reject your upload you will get notified next time you visit this site (requires cookies).
- Images larger than 800x600 pixels will automatically be reduced. So don't try to capture too much detail in a screenshot. It may become unreadable. Shrink the applications window if possible.
- Screenshots are made public and can freely be used by anyone.
- Useful programs for making screenshots are shutter, ksnapshot (KDE), gimp, xwd or scrot. See the Debian wiki for more information on how to make screenshots under Debian.
- Please set your language to english so that everybody understands it. If you don't use english by default please start your application from a shell using after setting "export LANG=C".