Biology subjects

Susan J Brown

Publications and source records attributed to Susan J Brown.

3 recordsLinked to original sources

bioRxiv2015

Fasta-O-Matic: a tool to sanity check and if needed reformat FASTA files

BackgroundAs the sheer volume of bioinformatic sequence data increases, the only way to take advantage of this content is to more completely automate robust analysis workflows. Analysis bottlenecks are often mundane and overlooked processing steps. Idiosyncrasies in reading and/or writing bioinformatics file formats can halt or impair analysis workflows by interfering with the transfer of data from one informatics tools to another.\n\nResultsFasta-O-Matic automates handling of common but minor format issues that otherwise may halt pipelines. The need for automation must be balanced by the need for manual confirmation that any formatting error is actually minor rather than indicative of a corrupt data file. To that end Fasta-O-Matic reports any issues detected to the user with optionally color coded and quiet or verbose logs.\n\nFasta-O-Matic can be used as a general pre-processing tool in bioinformatics workflows (e.g. to automatically wrap FASTA files so that they can be read by BioPerl). It was also developed as a sanity check for bioinformatic core facilities that tend to repeat common analysis steps on FASTA files received from disparate sources. Fasta-O-Matic can be set with format requirements specific to downstream tools as a first step in a larger analysis workflow.\n\nAvailabilityFasta-O-Matic is available free of charge to academic and non-profit institutions on GitHub.

Bioinformatics↗

bioRxiv2015

The Nicrophorus vespilloides genome and methylome, a beetle with complex social behavior

Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of genomes available for comparison spanning multiple independent lineages. For example, complex social behavior in insects has been investigated primarily with eusocial lineages, nearly all of which are Hymenoptera. If conserved genomic influences on sociality do exist, we need data from a wider range of taxa that also vary in their levels of sociality. Here we present information on the genome of the subsocial beetle Nicrophorus vespilloides, a species long used to investigate evolutionary questions of complex social behavior. We used this genome to address two questions. First, does life history predict overlap in gene models more strongly than phylogenetic groupings? Second, like other insects with highly developed social behavior but unlike other beetles, does N. vespilloides have DNA methylation? We found the overlap in gene models was similar between N. vespilloides and all other insect groups regardless of life history. Unlike previous studies of beetles, we found strong evidence of DNA methylation, which allows this species to be used to address questions about the potential role of methylation in social behavior. The addition of this genome adds a coleopteran resource to answer questions about the evolution and mechanistic basis of sociality.

Genomics↗

bioRxiv2015

Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool

BackgroundGenome assembly remains an unsolved problem. Assembly projects face a range of hurdles that confound assembly. Thus a variety of tools and approaches are needed to improve draft genomes.\n\nResultsWe used a custom assembly workflow to optimize consensus genome map assembly, resulting in an assembly equal to the estimated length of the Tribolium castaneum genome and with an N50 of more than 1 Mb. We used this map for super scaffolding the T. castaneum sequence assembly, more than tripling its N50 with the program Stitch.\n\nConclusionsIn this article we present software that leverages consensus genome maps assembled from extremely long single molecule maps to increase the contiguity of sequence assemblies. We report the results of applying these tools to validate and improve a 7x Sanger draft of the T. castaneum genome.

Bioinformatics↗