Apr 29, 2020

New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics

BioRxiv : the Preprint Server for Biology
Alexander KnyshovC. Weirauch

Abstract

Motivation: Despite many bioinformatic solutions for analyzing sequencing data, few options exist for targeted sequence retrieval from whole genomic sequencing (WGS) data. Available tools especially struggle at deep phylogenetic levels and necessitate amino-acid space searches, increasing rates of false positive results. Many such tools also suffer from difficult installation processes and lack adequate user resources. Results: Here, we describe a program using freely available similarity search tools to find homologs in assembled WGS data with unparalleled freedom to modify parameters. We evaluate its performance as well as that of other bioinformatics tools on two divergent insect species (>200 My) for which annotated genomes exist, as well as on one large set each of highly conserved and more variable loci. Our software is capable of retrieving orthologs from well-curated, low and high depth shotgun, and target capture assemblies as well or better than other software in finding the most genes with maximal coverage and has a low comparable rate of false positives throughout all datasets. Availability and Implementation: The software (implemented in Python), tutorials, and manual is freely available at https://github.com/AlexK...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

Standard of Care
Study
Biological Neural Networks
Follow-up
Glycine max
Soybean preparation
Neurons
Brain
Action Potentials
Soybean allergenic extract

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 Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

Related Papers

Physical Review A: General Physics
P BakK Wiesenfeld
The British Journal of General Practice : the Journal of the Royal College of General Practitioners
P Thomas
The British Journal of General Practice : the Journal of the Royal College of General Practitioners
T Holt
© 2020 Meta ULC. All rights reserved