Gepard [Mac/Win] ----------- Version 0.15.5 Change Log: ----------- 0.15.5 Change History --------------------------------------- - Fixed a bug in graph_dotplots that prevented sequences with more than one chromosome from being exported. - Set the style for plots of non-coding sequences to grey color by default. - Fixed a problem with size (in kb) in dotplots of very large sequences. - Fixed some problems with the nomenclature when displaying dotplots for multiple chromosomes. - Added a -nan option for points that will be shown at the location for a missing data value. 0.15.4 Change Log --------------------------------------- - Fixed a problem with the cgd file that prevented sequences from some species from being displayed correctly. - Improved the handling of chromosome boundaries in dotplots. - Improved the handling of large sequences. - Added a -nan option to use nad tags to indicate missing data. - Fixed a bug in the rendering of dotplots of very large sequences. - Fixed some issues in the displays of dotplots for multiple chromosomes. 0.15.3 Change Log --------------------------------------- - Fixed a bug in graph_dotplots that prevented sequences with size and coverage from being exported. - Improved the display of dotplots for large sequences (sizes >50kb). - Improved the alignment of sequences in dotplots. 0.15.2 Change Log --------------------------------------- - Fixed a bug that prevented sequences with larger sizes and larger coverage from being exported. - Fixed some problems in the display of dotplots for multiple chromosomes. 0.15.1 Change Log --------------------------------------- - Fixed a bug that prevented sequences with larger sizes and larger coverage from being exported. 0.15.0 Change Log --------------------------------------- - Added a new option to display the complete genome for a selected chromosome. - Improved the display of dotplots for multiple chromosomes. - Improved the alignment of sequences in dotplots. - Added a new option to align sequences in dotplots based on their names, using the nad2align program. - Added a new option to display the length of sequences in dotplots (as number of bases). - Added a new option to display the coverage of a sequence in a dotplot (as fraction of the genome). - Added a new option to display the size of Gepard Cracked Gepard With Keygen is a simple tool for analyzing sequence data (dotsplots) in chromosomal and bacterial genomes. It is primarily intended to be a tool for analyzing sequence data from contigs from shotgun sequencing data, but it can also be used for plotting the Dotplots obtained from long reads produced by the Long-read Sequencing Technology. Gepard can be used to verify if contigs are properly placed, and to check the overall quality of the assembly. By simply entering the sequence data Gepard will create a dotplot, and it can be used to calculate the amount of genome similarity between two sequence data sets. Gepard is free software (most common for DOS systems, but also available for Windows and Mac OS X) and can be downloaded at the link below. Gepard requires Microsoft Excel or another spreadsheet program to visualize the results. Gepard is most commonly used for alignments between genomes, so it can be used to analyze contigs from an assembly. Gepard is not intended to be used to analyze Sequence Reads. Download Gepard: Usage Instructions: Gepard accepts two sequence files to analyze: 1. A dotplot file, or a series of dotplot files 2. A pair of chromosomes to be compared To use Gepard with a dotplot file: Launch Gepard, and select the option to "Add files". You will then see a dialog box to browse for the dotplot files. The dotplots must be in.rdf format, or the appropriate save format will not work. 3. Click the button to open the file and add the dotplots to the analysis, and then close Gepard. 4. To view the results, start Excel or another spreadsheet program and click the "Add the Analysis" button under the "Control Panel". Excel should open with the Dotplot Analysis Spreadsheet. Analyzing Plots with Gepard: A dotplot for DNA sequence alignment is made from two chromosomes, A and B. Gepard works with sequences of any size, as it is simply a representation of the 1D sequence for each chromosome. Since Gepard is a tool for aligning sequences, the sequence for each chromosome is defined by two "pieces". In the following example, the sequence of each chromosome was defined by taking the first 5500 base pairs for chromosome A, and then the first 500 base pairs for chromosome B. +-----------+-----------+------------+ | Chromosome | Sequence A | Sequence B | +-----------+-----------+------------+ | A | 1a423ce670 Gepard Crack+ Free Download For Windows Developed by Dr. Adrian Preetorius. Dotplots can be used to visualize the relationship of two sequences. It is especially useful to analyze, align and visualize large sequences. If two sequences are concatenated, the dotplot resembles the typical DNA-molecular-wire-diagram. Chord diagrams display the different similarity blocks (hashes) in a sequence, which may be a meaningful analysis for the sequence. Comparative analysis of sequences is a powerful method to detect the common gene contents or function. The software is bundled with different dotplots for chromosomes or genomes and with a chord diagram. Currently, it is possible to represent the k-mer-frequency analysis with a chord diagram. With the chord diagram, it is possible to easily analyze the different regions of a sequence and the related gene functions. Further, the dotplot analysis allows the easy visualization of the k-mer-frequency analysis and the chord diagram. The software is designed as a non-commercial, desktop application which runs on Mac OS X, Windows (Vista) and Linux. Probabilities of the calculations are available and are based on simulations of 1 million kmers. Further, different background colours are available. Currently, the chord diagram is only available for mammalian sequences. But it is planned to add different bacterial genomes soon. Features: For example: 2 dotplots per sequence for chromosomes or for the complete genome 2 different dotplots (1 (complete) 2 (k-mer)-frequency analysis) Chord diagram (1 region) If the k-mer-frequency analysis does not have a region, a chord diagram can be calculated All operations can be done by an easy to use GUI The dotplot includes the following parameters: Left: Left border (default) The left border can be set manually or according to the window size W: Window size (defaults to 512 bp) It is possible to choose a different window size for the dotplot G: Gap size (default) The gap size is the distance between two regions, which have no bases in common. It is possible to define a maximum gap size S: Slide bar size (default) The slide bar size is the distance between the two windows. If it is not defined, a default value of 15 will be chosen. Right: Right border (default) What's New In? System Requirements For Gepard: Minimum Requirements: OS: Windows 10/8.1/8/7/XP (SP3) Processor: Intel Core i3-3220 (4GHz) Memory: 2 GB RAM Hard Disk: 5 GB available space Graphics: Intel HD Graphics 3000 DirectX: Version 11 Other: Recommended Requirements: Processor: Intel Core i5-2520M Memory
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