Apr 20, 2016

FGMP: assessing fungal genome completeness and gene content

BioRxiv : the Preprint Server for Biology
Ousmane Hamadoun Cisse, Jason Eric Stajich

Abstract

Motivation: Inexpensive high-throughput DNA sequencing has democratizing access to genetic information for most organisms so that access to a genome or transcriptome of an organism is not limited to model systems. However, the quality of the sampled genomes can vary greatly which hampers utility for comparisons and meaningful interpretation. The uncertainty of the completeness of a given genome sequence can limit feasibility of asserting patterns of high rates of gene loss reported in many lineages. Results: We propose a computational framework and sequence resource for assessing completeness of fungal genomes called FGMP (Fungal Genome Mapping Project). Our approach is based on evolutionary conserved sets of proteins and ultra conserved DNA elements and is applicable to various types of genomic data. We present a comparison of FGMP with state-of-the-art methods utilizing 246 genome assemblies of fungi. We discuss genome assembly improvements/degradations in 56 two-point fungal genome assemblies, as recorded by NCBI assembly archive. Availability and Implementation: FGMP software and datasets are freely available from https://github.com/stajichlab/FGMP or biocluster.ucr.edu/~ocisse/manuscript/FGMP.v.1.0.tar.gz Contact: ousmanec...Continue Reading

  • References
  • Citations

References

  • We're still populating references for this paper, please check back later.
  • References
  • Citations

Citations

  • This paper may not have been cited yet.

Mentioned in this Paper

Computer Software
Genome
Genes
Ncbi Taxonomy
Genome Assembly Sequence
Genome Mapping
Genomics
Genome, Fungal
Genomic DNA
Organism

About this Paper

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

© 2020 Meta ULC. All rights reserved