Functional annotation software tools | Shotgun metagenomic sequencing data analysis
Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex).
Allows analysis, integration, and interpretation of data derived from omics experiments. IPA is a web-based software application which identifies key regulators and activity to explain expression patterns, predicts downstream effects on biological and disease processes, provides targeted data on genes, proteins, chemicals, and drugs and builds interactive models of experimental systems. The analysis and search tools can uncover the significance of data and identify new targets or candidate biomarkers within the context of biological systems.
Allows users to taxonomically and functionally explore and analyze large-scale microbiome sequencing data. MEGAN is a comprehensive microbiome analysis toolbox for metagenome, meta-transcriptome, amplicon and from other sources data. Users can perform taxonomic, functional or comparative analysis, map reads to reference sequences, reference-based multiple alignments and reference-guided assembly and integrate their own classifications.
Allows users to obtain biological features/meaning associated with large gene or protein lists. DAVID can determine gene-gene similarity, based on the assumption that genes sharing global functional annotation profiles are functionally related to each other. It groups related genes or terms into functional groups employing the similarity distances measure. This tool takes into account the redundant and network nature of biological annotation contents.
Automatically assigns K numbers to genes in the genome, enabling reconstruction of KEGG pathways and BRITE hierarchies. The method is based on sequence similarities, bi-directional best hit information and some heuristics, and has achieved a high degree of accuracy when compared with the manually curated KEGG GENES database.
Scans sequences against InterPro's signatures. InterProScan allows users to characterize a nucleotide or protein function by matching it with models from several different databases and to obtain a better overview of their results. The software performs relatively small numbers of sequences in a single analysis, including the ability to parallelize search jobs to minimize wall-clock time.
Consists of a one-stop online assembly of computational software tools. ToppGene Suite enables users to (i) perform gene list enrichment analysis, (ii) perform candidate gene prioritization based on functional annotations, (iii) perform candidate gene prioritization based on protein interactions network analysis and (iv) identify and rank candidate genes in the interactome based on both functional annotations and e protein-protein interaction network (PPIN) analysis. The suite can identify true candidate genes.
Assists users in performing microbial genome annotation, data management and comparative analysis. MicroScope furnishes an environment permitting researchers to perform specifically comparative analysis of prokaryotic genomes, and manual curation of gene function in a comparative genomics and metabolic context. Moreover, this tool was used for annotating microbial genomes, transcriptomic and re-sequencing data.