Gepard is a free Java software which allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes.
Use cases:
· Online comparison of partial or complete genomes from the PEDANT databases without downloading any sequence data.
· Online comparison of a user-supplied nucleotide sequence against a genome from the PEDANT database.
· Local comparison two of nucleotide or amino acid sequences from user-specified files.
· Batch dotplot functionality provided by command line access to Gepard
Here are some key features of "Gepard":
· Rapid calculation of dotplots ( simply specify two sequences and create the dotplot (3 clicks)
· Easy-to-use interface (mouse zooming, context-sensitive help)
· Image exports (multiple formats)
· Should work on any common OS due to Java software architecture
· Genes covered by the dotplot are linked to their report webpages in the PEDANT database
· Coloring of genes by functional classification (uses data from PEDANT)
· Persistent storage of suffix arrays (avoids recalculation)
Requirements:
· Java 1.5 or later
What's New in This Release: [ read full changelog ]
· PEDANT3 integration for remote functionality implemented
· => pedant.gsf.de
· new functions for multi-FASTA files (sequence name is displayed in the dot-
· plot while moving the mouse over the plot)
· bug in FASTA reader fixed
· corrected GUI display errors on Mac OS X
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