Package: lifton
LiftOn is a homology-based lift-over tool designed to accurately map annotations in GFF or GTF between assemblies. It is built upon the fantasticLiftoff(credits toDr. Alaina Shumate) andminiprot(credits toDr. Heng Li), and employs aProtein-maximization algorithmto improve the protein-coding gene lift-over process.Why LiftOn❓#Burgeoning number of genome assemblies: As of December 2023, among the 15,578 distinct eukaryotic genomes, only 1,111 have been annotated (Eukaryotic Genome Annotation at NCBI). More and more high quality assemblies are generated. We need to accurately annotate them.Improved protein-coding gene mapping: The popularLiftoffmap genes only based on the DNA alignment. With the protein-to-genome alignment, LiftOn is able to further improve the lift-over protein-coding gene annotations. LiftOn improves the current released T2T-CHM13 annotation (JHU RefSeqv110 + Liftoff v5.1).Improved distant species lift-over: LiftOn extends from lift-over between the same or closely related species to more distantly related species. Seemouse_2_ratanddrosophila_melanogaster_2_erectalift-over sections.LiftOn is free, it's open source, it's easy to install , and it's in Python!Who is it for❓#If you have sequenced and assembled a new genome and need to annotate it, LiftOn is the ideal choice for generating annotations.If you want to do comparative genomics analysis, run liftOn to lift-over and compare annotations!If you wish to utilize the finest CHM13 annotation, you can run LiftOn! We have also pre-generated theT2T_CHM13_LiftOn.gff3file for your convenience.What does LiftOn do❓#LiftOn is designed for individuals who would like to annotate a new assembly, referred to as targetGenomeT.The first step is to select a well-annotated genome along with its annotation, denoted as referenceGenomeRandAnnotationRA.LiftOn employs a two-stepProtein-maximization algorithm(PM algorithm).The first module is thechaining algorithm. It starts by extracting protein sequences annotated by Liftoff and miniprot. LiftOn then aligns these sequences to full-length reference proteins. For each gene locus, LiftOn compares each section of the protein alignments from Liftoff and miniprot, chaining together the best combinations.The second module is theopen-reading frame search (ORF search) algorithm. In the case of truncated protein-coding transcripts, this algorithm examines alternative frames to identify the ORF that produces the longest match with the reference protein.Input:targetGenomeTin FASTAreferenceGenomeRin FASTAreferenceAnnotationRAin GFF3Output:LiftOn annotation file in GFF3Protein sequence identities & mutation typesFeatures with extra copiesUnmapped featuresLiftOn's limitation#LiftOn'schaining algorithmcurrently only utilizes miniprot alignment results to fix the Liftoff annotation. However, it can be extended to chain together multiple protein-based annotation files or aasembled RNA-Seq transcripts.DNA- and protein-based methods still have some limitations. We are developing a module to merge the LiftOn annotation with the released curated annotations to generate better annotations.The LiftOnchaining algorithmnow does not support multi-threading. This functionality stands as our next targeted feature on the development horizon!User support#Please go through thedocumentationbelow first. If you have questions about using the package, a bug report, or a feature request, please use the GitHub issue tracker here:https://github.com/Kuanhao-Chao/LiftOn/issuesKey contributors#LiftOn was designed and developed byKuan-Hao Chao.  This documentation was written byKuan-Hao Chao.Table of contents#InstallationSystem requirementsInstall through pipInstall through condaInstall from sourceCheck LiftOn installationNow, you are ready to go !Quick Start GuideSuper-Quick Start (one-liner)Try LiftOn on Google ColabExamplesSame species lift-overClosely-related species lift-overDistant species lift-overInfoOutput fileslifton.GFF3lifton_output/Behind the scenesMatching miniprot & Liftoff genome annotationProtein-maximization algorithmMutation reportOpen-reading-frame searchDNA & protein transcript sequence identity score calculationReferenceQ & A ...User ManualsplamChangelogv1.0.0LicenseContactCitation#Kuan-Hao Chao*, Mihaela Pertea, Steven L Salzberg*, "LiftOn: a tool to improve annotations for protein-coding genes during the lift-over process.",bioRxiv2023.07.27.550754, doi:https://doi.org/10.1101/2023.07.27.550754, 2023