From: Solving the Problem: Genome Annotation Standards before the Data Deluge
Category/Title | Description | Reference | URL |
---|---|---|---|
General | Â | Â | Â |
NCBI Genome Annotation Workshop | All information from this publication, the Annotation Workshop, and futureannouncements will be made available | Â | |
Difference between Archive and Curated Databases | GenBank, RefSeq, TPA and UniProt:What’s in a Name? | Microbe Online | |
Difference between Archive and Curated Databases | GenBank, RefSeq, TPA and UniProt:What’s in a Name? | NCBI Handbook | http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook&part=ch1#GenBank_ASM |
INSDC | International Nucleotide Sequence Database Collaboration | Â | |
INSDC Feature Table | Feature table document | Â | |
DDBJ | DNA Databank of Japan | [35] | |
ENA | European Nucleotide Archive | [36] | |
GenBank | GenBank | [20] | |
Automated Annotation providers | Â | Â | Â |
NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) | Intended for use during the annotation of prokaryotic genomes in preparation for submission to GenBank — capable of annotating complete genomes as wells WGS genomes |  | |
JCVI Annotation Service | Anyone with a prokaryotic genome sequence in need of annotation may submit it to the JCVI Annotation Service completely free-of-charge | Â | http://www.jcvi.org/cms/research/projects/annotation-service/overview |
IGS Annotation Engine | A free resource for genomics researchers and educators bringing advanced bioinformatics tools to the lab bench and the classroom. | Â | |
KAAS - KEGG Automatic Annotation Server | KAAS (KEGG Automatic Annotation Server)provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database with resulting KO (KEGG Orthology) assignments and automatically generated KEGG pathways | [37] | |
RAST | RAST (Rapid Annotation using Subsystem Technology) is a fully automated service for annotating bacterial and archaeal genomes — provides high quality genome annotations for these genomes across the whole phylogenetic tree | [38] | |
DOE-JGI MAP | Expert Review Data Submission: Microbial Genomes & Management | [39] | |
Annotation Cleanup, Analyses, and Validation Tools | Â | Â | Â |
NCBI Submission Check Tool | For the validation of genome submissions to GenBank — utilizes a series of self-consistency checks as well as comparison of submitted annotations to computed annotations — web-based and downloadable versions available |  | http://www.ncbi.nlm.nih.gov/genomes/frameshifts/frameshifts.cgi |
NCBI Sequin Validation | Sequin is a standalone tool for submitting and updating sequences | [20] | |
NCBI TBL2ASN | Command-line tool for automation of sequence records to GenBank | [20] | |
NCBI Discrepancy report | Evaluation of ASN.1 files for annotation discrepancies-part of Sequin, available separately as downloadable command line version, and part of tbl2asn | [20] | |
Broad’s Gene Pidgin (formerly BioName) | A free resource for genomics researchersand educators bringing advanced bioinformaticstools to the lab bench and the classroom. |  | |
JCVI’s Protein Naming Utility | KAAS (KEGG Automatic Annotation Server) provides functional annotation of genes by BLAST comparisons against themanually curated KEGG GENES database with resultingKO (KEGG Orthology) assignments andautomatically generated KEGG pathways | [37] | |
Frameshift Tool | RAST (Rapid Annotation using Subsystem Technology) is afully-automated service for annotating bacterial andarchaeal genomes — provides high quality genome annotations forthese genomes across the whole phylogenetic tree | [38] | |
Annotation Report | Expert Review Data Submission: Microbial Genomes & Management | ||
Annotation Guidelines | Â | Â | Â |
GenBank Bacterial Genome Submission Guidelines | For the validation of genome submissions to GenBank-utilizes a series of self-consistency checksas well as comparison of submitted annotations tocomputed annotations — web-based anddownloadable versions available |  | http://www.ncbi.nlm.nih.gov/genomes/frameshifts/frameshifts.cgi |
Annotation Instructions | Sequin is a standalone tool for submittingand updating sequences | [20] | |
Project Submission | Command-line tool for automation of sequencere-cords to GenBank | [20] | |
Locus_tag proposal | Evaluation of ASN.1 files for annotation discrepancies-part of Sequin, available separately as downloadablecommand line version, and part of tbl2asn | [20] | |
UniProt’s Protein Naming Guidelines | UniProt’s prokaryotic-specific protein naming guidelines — adopted by INSDC |  | |
GSC Structured Format | Accepted structured format for genome metadata including SOPs | [43] | |
Insertion Sequences | Insertion sequence finder, nomenclature, and registry | [44] | |
Transposons | Transposon nomenclature and registry | [45] | |
Enzyme Commission Numbers | Official NC-IUBMB site | Â | |
UniProt ENZYME | ENZYME is a repository of information relative to the nomenclature of enzymes. | Â | |
Functional Annotation/Protein Families | Â | Â | Â |
NCBI COGs | Clusters of orthologous groups - no longer actively curated | [46] | |
NCBI ProtClustDB | Cliques of related proteins — curated and uncurated — for multiple organism groups including prokaryotes and Viruses | [33] | |
NCBI Cluster Comparison Tool | Protein family comparison for functional annotation | Â | |
NCBI Cluster Comparison Tool - Core Mode | Protein family core comparison for functional annotation | Â | |
List of Core Clusters | Protein family core list | Â | http://www.ncbi.nlm.nih.gov/sutils/clustcomp.cgi?report=core |
UniProt HAMAP | system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies in prokaryotes and plastids | [47] | |
KEGG Orthology Groups | Manually defined ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes | [48] | |
JCVI’s TIGRFAMs | Protein families based on Hidden Markov Models | [49] | http://www.jcvi.org/cms/research/projects/tigrfams/overview/ |
ACLAME | Database dedicated to the collection and classification of mobile genetic elements | [50] | |
E. coli CCDS Project | Comparison of annotation for model E. coli K-12 MG1655 | Â |