Gene orthology detection software tools | High-throughput sequencing data analysis
Gene orthology aims at identifying evolutionary relationships between genes from different species. Identification of orthologous gene sets typically involves phylogenetic tree analysis, heuristic algorithms based on sequence conservation, synteny analysis, or some combination of these approaches.
Searches protein database using a translated nucleotide query. BLASTX is a BLAST search application that compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database. This application can also work in Blast2Sequences mode and can send BLAST searches over the network to public NCBI server if desired.
Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. BUSCO assessments are implemented in open-source software, with comprehensive lineage-specific sets of benchmarking universal single-copy orthologs for arthropods, vertebrates, metazoans, fungi, eukaryotes, and bacteria.
A web server that performs automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. BASys uses more than 30 programs to determine nearly 60 annotation subfields for each gene, including gene/protein name, GO function, COG function, possible paralogues and orthologues, molecular weight, isoelectric point, operon structure, subcellular localization, signal peptides, transmembrane regions, reactions, and pathways. The textual annotations and images that are provided by BASys can be generated in approximately 16 hours for an average bacterial chromosome (5 Megabases. 5000 genes), or approximately 350 coding regions per hour.
Converts genome coordinates and genome annotation files between assemblies. UCSC LiftOver is a pipeline that can be used to convert coordinate ranges between genome assemblies. It supports forward/reverse conversions, batch conversions, and conversions between species.
A toolkit that implements an adjusted MCScan algorithm for detection of synteny and collinearity and incorporates 14 computer programs for visualizing and analyzing identified synteny and collinearity. MCScanX scans multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and aligns these regions using genes as anchors. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families.
Identifies orthologous protein sequence families. OrthoFinder provides a three-steps method that first perform orthogroup inference, then, it deduces rooted species and gene trees for lastly determine orthologs and gene duplication events from these rooted gene trees. The application is able to produce a wide of outputs including orthogroups and their gene trees, the rooted species tree, gene duplication events, as well as comparative genomics statistics.