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Abstract Detail



Genomics / Proteomics

Veltri, Daniel [1], Malapi-Wight, Martha [2], Crouch, Jo Anne [3].

Simple Synteny: An accessible tool for comparisons of genomic regions.

Genomic comparison is a common task for biologists, and particularly important for studying chromosomal rearrangements, gene clusters, and genome evolution. While there are a number of programs currently available for generating syntenic maps, many are inaccessible to biologists who lack the required computer or scripting skills needed for proper installation or data preprocessing. Most available tools require a trade-off between annotation detail and visual scale; often, showing acute annotations at the nucleotide level and more obtuse detail for contigs. Many programs particularly suffer when they zoom out to a higher level view yet attempt to maintain low-level connections between loci. These connecting lines can blur together and make an image rather ambiguous for the viewer. We present here Simple Synteny, a free and open-source image generator for use in syntenic analysis. Simple Synteny provides an easy interface for comparing multiple genomes by only requiring the user to submit FASTA files for the genomes and genes of interest. This work presents a new pipeline for automating the production of images, providing output that is clearer and more comprehensible for comparing genomic regions. In particular, we focus on visualizing between one and ten contigs for up to six taxa of interest. The program employs gene color coordination across genomes, indicator arrows for changes in gene direction and automatic contig and gene resizing to produce publication-quality images which are clear and simple to interpret. The ultimate goal of this work is to present biologists with a useful tool for quickly generating genomic comparison figures for publication without the need for laborious manual annotation in programs such as PowerPoint or Photoshop. Directions for using the tool and example analyses are provided.


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Related Links:
Crouch Lab


1 - USDA-ARS, 10300 Baltimore Avenue, Building 010A, Beltsville, MD, 20705
2 - USDA-ARS, 10300 Baltimore Avenue, Building 010A, Beltsville, MD, 20705, USA
3 - USDA-ARS, Systematic Mycology & Microbiology, 10300 Baltimore Avenue, Building 010A, Beltsville, MD, 20705, USA

Keywords:
Comparative Genomics
Bioinformatics
Fungi
syntenic analysis
Calonectria
Colletotrichum.

Presentation Type: Poster:Posters for Topics
Session: P
Location: Hall D/The Shaw Conference Centre
Date: Monday, July 27th, 2015
Time: 5:45 PM
Number: PGP014
Abstract ID:1310
Candidate for Awards:None


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