Comparative Genomics

Some of the tools in KBase available for comparative genomics and phylogenetics

KBase provides multiple comparative genomics and phylogenetic analysis Apps to enable researchers to understand evolutionary relationships between organisms and explore structural and functional variance across genomes.

Phylogenetic and Taxonomic Analysis

• Insert Genome Into Species Tree – Build a phylogenetic tree with your genomes and RefSeq microbial genomes based on conserved orthologous groups

• Build Microbial Species Tree (in beta) – Build a phylogenetic tree with your genome and phylum exemplars from RefSeq

• Build Gene Tree (in beta) – Build an evolutionary reconstruction tree for a collection of sequence homology related genes

• Build Phylogenetic Tree with FastTree2 – Build a tree with FastTree2 directly on a user-created Multiple Sequence Alignment (MSA)

Sequence Homology and Functional Analysis

• BLASTx, tBLASTn, and tBLASTx – Search genes in genomes and Annotated Metagenome Assemblies (AMAs) and compare translated protein sequences

• BLASTn – Search genes and AMAs and compare nucleotide sequences

• BLASTp and psiBLAST – Search genes and AMAs and compare protein sequences

• MUSCLE for nucleotide or protein sequences – Build and analyze multiple sequence alignments (MSA)

• HMMER MSA Collection – Search and profile genes in genomes and Annotated Metagenome Assemblies (AMAs) with a collection of user-defined MSAs

  • HMMER Search from MSA – Search genes in genomes and AMAs with a single user-defined MSA

  • HMMER Search with dbCAN2 of CAZy families – Search and profile genes in genomes and AMAs with the suite of CAZy dbCAN2 hidden markov models (HMMs)

  • HMMER Search for Phylo Markers – Search and profile genes in genomes and AMAs with the suite of GTDB protein phylogenetic marker HMMs

  • HMMER Search for Env BioElement families – Search and profile genes in genomes and AMAs with the suite of Environmental BioElement metabolic families

• Annotate Domains in a GenomeSet – Compute canonical gene family membership using COG, Pfam, and TIGRFAMs

• View Function Profile for Genomes and View Function Profile for a Phylogenetic Tree – Examine functional content from canonical domain family annotation

Pangenome Exploration

• Compare Two Proteomes – Compare proteomes and produce a synteny map dot plot matrix and table of gene differences
• Build Pangenome with OrthoMCL – Group orthologous protein sequences and identify core and non-core genes across multiple species
• Calculate Pangenome wiht mOTUpan - Calculate pangenome for microbial genomes, including MAGs of varying quality
• Compute Pangenome – Build a pangenome and evaluate protein family conservation
• Pangenome Circle Plot – View a microbial pangenome as a circle plot using
• Compare Genomes from Pangenome – Compare isofunctional and homologous gene families within a pangenome
• Phylogenetic Pangenome Accumulation – View the pangenome in a phylogenetic context