ArticleG3 (Bethesda, Md.)2017
KinFin: Software for Taxon-Aware Analysis of Clustered Protein Sequences.
Article in G3 (Bethesda, Md.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- Chromosome-level genome assembly of Tamarindus indica provides new insights into the evolution of triterpenes and tartaric acid biosynthetic pathway.Molecular horticulture · 2026Article
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- MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot microchromosomes.GigaScience · 2026Article
- Genome assembly and insights into globally invasive Red-vented Bulbul (Pycnonotus cafer).DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Life inside a bag: multiomics insights into the bagworm species Eumeta crameri.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Wolbachia Host Shifts and Widespread Occurrence of Reproductive Manipulation Loci in European Butterflies.Molecular ecology · 2025Article
- Hemipteran insects experience recurrent and synergistic molecular evolution adapting to diet shift.BMC biology · 2025Article
- Bryophytes hold a larger gene family space than vascular plants.Nature genetics · 2025Article
- Assembly and annotation of Solanum dulcamara and Solanum nigrum plant genomes, two nightshades with contrasting susceptibilities to Ralstonia solanacearum.G3 (Bethesda, Md.) · 2025Article
- A high-quality genome assembly of Annona squamosa (custard apple) provides functional insights into an emerging fruit crop.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Molecular evolution of dietary shifts in ladybird beetles (Coleoptera: Coccinellidae): from fungivory to carnivory and herbivory.BMC biology · 2025Article
- Massive Gene Loss in the Fungus Sporothrix epigloea Accompanied a Shift to Life in a Glucuronoxylomannan-based Gel Matrix.Genome biology and evolution · 2025Article
- A high-quality chromosome-level genome assembly of the oligophagous fruit fly Bactrocera tsuneonis (Diptera: Tephritidae) and insights into its host specificity.GigaScience · 2025Article
- Transcriptome sequencing data provide a solid base to understand the phylogenetic relationships, biogeography and reticulated evolution of the genus Zamia L. (Cycadales: Zamiaceae).Annals of botany · 2024Article
- Ancient Secretory Pathways Contributed to the Evolutionary Origin of an Ecologically Impactful Bioluminescence System.Molecular biology and evolution · 2024Article
- Phage biocontrol success of bacterial wilt depends on synergistic interactions with resident rhizosphere microbiota.Microbial biotechnology · 2024Article
- Genome of the most noxious weed water hyacinth (iScience · 2024Article
- The adult shell matrix protein repertoire of the marine snail Crepidula is dominated by conserved genes that are also expressed in larvae.BMC ecology and evolution · 2024Article
- Article
- Selection and Gene Duplication Associated With High-Elevation Diversification in Pristimantis, the Largest Terrestrial Vertebrate Genus.Genome biology and evolution · 2024Article
2 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
The field of comparative genomics is concerned with the study of similarities and differences between the information encoded in the genomes of organisms. A common approach is to define gene families by clustering protein sequences based on sequence similarity, and analyze protein cluster presence and absence in different species groups as a guide to biology. Due to the high dimensionality of these data, downstream analysis of protein clusters inferred from large numbers of species, or species with many genes, is nontrivial, and few solutions exist for transparent, reproducible, and customizable analyses. We present KinFin, a streamlined software solution capable of integrating data from common file formats and delivering aggregative annotation of protein clusters. KinFin delivers analyses based on systematic taxonomy of the species analyzed, or on user-defined, groupings of taxa, for example, sets based on attributes such as life history traits, organismal phenotypes, or competing phylogenetic hypotheses. Results are reported through graphical and detailed text output files. We illustrate the utility of the KinFin pipeline by addressing questions regarding the biology of filarial nematodes, which include parasites of veterinary and medical importance. We resolve the phylogenetic relationships between the species and explore functional annotation of proteins in clusters in key lineages and between custom taxon sets, identifying gene families of interest. KinFin can easily be integrated into existing comparative genomic workflows, and promotes transparent and reproducible analysis of clustered protein data.
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