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Functional annotation programs

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Vikodak
Web

Vikodak

A multi-modular package that is based on the above assumption and automates…

A multi-modular package that is based on the above assumption and automates inferring and/ or comparing the functional characteristics of an environment using taxonomic abundance generated from one…

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InterProScan
Desktop
Web

InterProScan

Scans sequences against InterPro's signatures. InterProScan allows users…

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…

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GhostKOALA
Web

GhostKOALA

Allows metagenome annotation. GhostKOALA is an automatic annotation server that…

Allows metagenome annotation. GhostKOALA is an automatic annotation server that utilizes the GHOSTX program for searching the non-redundant GENES database. The software is recommended for annotating…

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biomartr
Desktop

biomartr

Provides a comprehensive easy-to-use framework for automating data retrieval…

Provides a comprehensive easy-to-use framework for automating data retrieval and functional annotation for meta-genomic approaches. The biomartr package implements straightforward functions for bulk…

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SALT
Desktop

SALT

A protein domain classification tool based on profile hidden Markov models and…

A protein domain classification tool based on profile hidden Markov models and graph algorithms. SALT carefully incorporates the characteristics of reads that are sequenced from the domain regions…

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MetaStorm
Web

MetaStorm

Offers both read matching and assembly-based annotation pipelines. MetaStorm is…

Offers both read matching and assembly-based annotation pipelines. MetaStorm is an online metagenomic analysis server. It enables customization of reference databases and allows users to upload…

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Fun4Me
Desktop

Fun4Me

Infers protein-coding genes, and their putative functions from metagenomic…

Infers protein-coding genes, and their putative functions from metagenomic datasets. Fun4Me is a pipeline for functional annotation of metagenomes. It is built upon several computational tools…

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ROCker
Desktop

ROCker

Employs the receiver operating characteristic curve to minimize false discovery…

Employs the receiver operating characteristic curve to minimize false discovery rate (FDR). ROCker is an automated bioinformatic pipeline that calculates the best thresholds based on how simulated…

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UProC
Desktop

UProC Ultrafast Protein Classification

This toolbox implements an algorithm ("Mosaic Matching") for…

This toolbox implements an algorithm ("Mosaic Matching") for large-scale sequence analysis. UProC is by three orders of magnitude faster than profile-based methods and in a metagenome…

Qnr-search
Desktop

Qnr-search

A method to detect and annotate novel classes of qnr antibiotic resistance…

A method to detect and annotate novel classes of qnr antibiotic resistance genes in nucleotide sequence data. Qnr-search uses a hidden Markov model with a fragment length-dependent classification…

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COGNIZER
Desktop

COGNIZER

A comprehensive stand-alone annotation framework which enables end-users to…

A comprehensive stand-alone annotation framework which enables end-users to functionally annotate sequences constituting metagenomic datasets. The COGNIZER framework provides multiple workflow…

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Woods
Desktop
Web

Woods

An orthology-based functional classifier by using a combination of machine…

An orthology-based functional classifier by using a combination of machine learning and similarity-based approaches. Woods displayed a precision of 98.79% on independent genomic dataset, 96.66% on…

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RTMg
Desktop
Web

RTMg Real Time Metagenomics

Generate functional annotations for metagenomes (random community genomes)…

Generate functional annotations for metagenomes (random community genomes) using k-mer based comparisons to amino acid sequences. Fast, accurate, and comparable. Upload multiple sequences and see…

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MetaSAMS
Web

MetaSAMS

A software platform for automated taxonomic and functional analysis of…

A software platform for automated taxonomic and functional analysis of metagenome data. MetaSAMS includes a pipeline consisting of three different classifiers that perform taxonomic profiling of…

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