Biology subjects

Andorf, C.

Publications and source records attributed to Andorf, C..

2 recordsLinked to original sources

bioRxiv2025

MaizeGDB Phylostrata Tool: Exploring evolutionary origins of maize proteins

MotivationPhylostratigraphic analysis identifies the evolutionary origins and level of conservation of proteins, facilitating research in evolutionary biology and comparative genomics. ResultsWe developed the MaizeGDB Phylostrata Tool, a custom web application that enables users to explore the evolutionary origins of maize proteins. This tool features interactive visualizations and detailed gene pages incorporating subcellular localization, Gene Ontology (GO) terms, and other resources for homologs. Full-proteome downloads are available for 26 maize inbreds (B73 and the NAM founders). We also provide an updated version of the phylostratr R package that makes it more robust to taxonomic updates, as well as example scripts for phylostratigraphic analysis and webtool development for the use of researchers and curators of other species. Availability and ImplementationThe MaizeGDB Phylostrata Tool is freely available at phylostrata.maizegdb.org. Scripts used for the analysis and web tool are available at https://github.com/LTibbs/PhylostrataWebtool. Contactcarson.andorf@usda.gov

bioinformatics↗

bioRxiv2022

ABRIDGE: An ultra-compression software for SAM alignment files

Advancement in technology has enabled sequencing machines to produce vast amounts of genetic data, causing an increase in storage demands. Most genomic software utilizes read alignments for several purposes including transcriptome assembly and gene count estimation. Herein we present, ABRIDGE, a state-of-the-art compressor for SAM alignment files offering users both lossless and lossy compression options. This reference-based file compressor achieves the best compression ratio among all compression software ensuring lower space demand and faster file transmission. Central to the software is a novel algorithm that retains non-redundant information. This new approach has allowed ABRIDGE to achieve a compression 16% higher than the second-best compressor for RNA-Seq reads and over 35% for DNA-Seq reads. ABRIDGE also offers users the option to randomly access location without having to decompress the entire file. ABRIDGE is distributed under MIT license and can be obtained from GitHub (https://github.com/sagnikbanerjee15/Abridge) and docker hub. We anticipate that the user community will adopt ABRIDGE within their existing pipeline encouraging further research in this domain.

bioinformatics↗