GEL personnel are currently engaged in developing a number of software tools that may be of interest to other researchers.  Here we highlight some of the tools we have developed.
  • ASAP - A Systematic Annotation Package for Community Analysis of Genomes

    ASAP is designed to organize the data associated with a genome from the early stages of sequence annotation through genetic and biochemical characterization, providing a vehicle for ongoing updates of the annotation and a repository for genome-scale experimental data. Development was motivated by the need to more directly involve a greater community of researchers, with their collective expertise, in keeping the genome annotation current and to provide a synergistic link between up-to-date annotation and functional genomic data.

  • Mauve - Multiple Genome Alignment

    Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics on a new scale. Aligning whole genomes is a fundamentally different problem than aligning short sequences.

    Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours.

  • GRIL - Genome Inversion and Rearrangement Locator

    GRIL is a tool that can be used to identify the location of rearrangements and inversions in the backbone of a set of DNA sequences. GRIL works by identifying exactly matching regions present in all sequences under consideration and organizing them into groups of collinear regions. GRIL removes small regions of collinearity that appear unlikely to be true sequence rearrangements based on user-specified criteria such as the length of the collinear region and the percent sequence identity of the collinear region. The size of sequences that GRIL can be applied to is dependent on the amount of available memory.

  • Software Development Libraries
    We have created several software development libraries that other developers may find useful.
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