Tool |
Description/Features |
Web Address/URL |
Ref. |
| |
Assembly Tools |
|
|
| CAP3 |
Alignment/assembly/Roche |
http://pbil.univ-lyon1.fr/cap3.php |
|
| Abyss |
Alignment/assembly/Illumina |
www.bcgsc.ca/platform/bioinfo/software/abyss |
|
| Phrap |
Alignment/assembly/Illumina/Roche |
http://www.phrap.org/consed/consed.html |
|
| Velvet |
Alignment/assembly/Roche/ABI/Illumina |
http://www.ebi.ac.uk/%7Ezerbino/velvet |
|
| |
Gene Prediction Tools |
|
|
| Glimmer |
Microbial gene-finding system |
www.cbcb.umd.edu/software/glimmer/ |
[103] |
| GeneMark |
Gene Prediction in Bacteria, Archaea and Metagenomes |
http://opal.biology.gatech.edu/GeneMark/ |
[18] |
| EasyGene |
Gene Predictor in prokaryotic DNA |
www.cbs.dtu.dk/services/EasyGene/ |
[43] |
| FgenesB |
Bacterial Operon and Gene Prediction |
http://linux1.softberry.com/ |
[104] |
| REGANOR |
Gene prediction Sever and Database |
www.cebitec.uni-bielefeld.de/ |
[69] |
| Prodigal |
Prokaryotic Dynamic Programming Gene finding Algorithm |
http://prodigal.ornl.gov/ |
[105] |
| |
Automatic and Manual Annotation Pipelines/Tools |
|
|
| GenColors |
Comparative Genomics and Annotation Tool |
http://gencolors.imb-jena.de/ |
[5] |
| MicroScope |
Comparative Genomics and Annotation Platform |
http://www.genoscope.cns.fr/ |
[6] |
| KAAS |
KEGG Automatic Annotation Server |
www.genome.jp/tools/kaas/ |
[23] |
| AutoFACT |
Automated Annotation Tool |
http://megasun.bch.umontreal.ca/ |
[25] |
| BASys |
Bacterial Annotation System |
http://basys.ca/basys/cgi/submit.pl |
[42] |
| IGS |
IGS Prokaryotic Annotation Pipeline |
http://ae.igs.umaryland.edu/cgi/ |
[26] |
| CMR |
Comprehensive Microbial Resource and annotation |
http://cmr.jcvi.org/ |
[27] |
| PGAAP |
NCBI Prokaryotic Automatic Annotation Pipeline |
www.ncbi.nlm.nih.gov/genomes/ |
[28] |
| GenDB |
Prokaryotic Genomes Annotation System |
www.cebitec.uni-bielefeld.de/ |
[15] |
| MANATEE |
Manual Functional Annotation Tool |
http://manatee.sourceforge.net/ |
[41] |
| HAMAP |
Automated and Manual Annotation of Microbial Proteomes |
http://us.expasy.org/sprot/hamap/ |
[2] |
| RAST |
Rapid Annotation using Subsystem Technology |
www.nmpdr.org/FIG/wiki/view.cgi/ |
[9] |
| xBASE |
Bacterial Genome Annotation Service |
http://www.xbase.ac.uk/annotation/ |
[42] |
| Blast2GO |
Annotation and Sequence Analysis tool |
http://www.blast2go.com/ |
|
| |
Databases and Resources |
|
|
| NCBI |
Genbank, RefSeq, TPA and PDB, databanks for storage and downloadable genomic information |
http://www.ncbi.nlm.nih.gov/ |
|
| EMBL |
Nucleotide Sequence Database |
http://www.ebi.ac.uk/embl |
|
| GOLD |
Data resource for genomic and matagenomic projects |
http://www.genomesonline.org/ |
|
| KEGG |
An integrated database resource, provides genomic, chemical and systemic information |
http://www.kegg.jp/ |
|
| IMG |
Resource for Comparative Analysis and Annotation |
http://img.jgi.doe.gov/ |
|
| JCVI |
Comprehensive Microbial Resource (CMR) |
http://www.jcvi.org/ |
|
| MBGD |
Database, analysis of orthologous, paralogous, motifs, gene order and annotation. |
http://mbgd.genome.ad.jp/ |
|
| RDP |
Ribosomal Database, bacterial RNA sequences, alignments and tools for RNA analysis |
http://rdp.cme.msu.edu/ |
|
| Rfam |
RNA database |
http://rfam.sanger.ac.uk/ |
|
| GtRNAdb |
RNA Database, tRNA gene Predictions |
http://lowelab.ucsc.edu/GtRNAdb/ |
|
| UniProt |
Protein Resource and Functional information |
http://www.uniprot.org |
|
| UniProtKB |
Curated Protein Database (UniProtKB/Swiss-Prot and UniProtKB/TrEMBL) |
http://www.uniprot.org/help/uniprotkb |
|
| Gene Ontology (GO) |
GO Database, annotation of genes, protein and sequences. |
http://www.geneontology.org/ |
|
| METACYC |
Database for metabolic pathways |
http://metacyc.org/ |
|
