Skip to main content

Advertisement

Table 1 List of software and databases incorporated in the DeNoGAP pipeline

From: A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies

Program Names Website Reference
Gene Prediction
Glimmer http://ccb.jhu.edu/software/glimmer/index.shtml [15]
FragGeneScan http://omics.informatics.indiana.edu/FragGeneScan/ [18]
Prodigal https://github.com/hyattpd/Prodigal [17]
GeneMark http://opal.biology.gatech.edu/GeneMark/ [16]
Sequence Comparison   
BLAST ftp://ftp.ncbi.nlm.nih.gov/blast [22]
HMMER http://hmmer.org [27]
Multiple Alignment
Muscle http://www.drive5.com/muscle [29]
Kalign http://www.ebi.ac.uk/Tools/msa/kalign [32]
Distance Matrix
Phylip http://evolution.gs.washington.edu/phylip [33]
Clustering
Markov chain Clustering (MCL) http://micans.org/mcl [28]
Sequence manipulation
EMOSS http://emboss.sourceforge.net [20]
Functional Annotation
InterProScan https://code.google.com/p/interproscan/ [40]
Annotation Database
UniprotKB / SwissProt http://www.uniprot.org [19]
Pfam http://pfam.xfam.org [41]
Gene3D http://gene3d.biochem.ucl.ac.uk/Gene3D/ [42]
SMART http://smart.embl-heidelberg.de [43]
ProDOM http://prodom.prabi.fr/prodom/current/html/home.php [44]
FingerPRINTScan http://www.ebi.ac.uk/Tools/pfa/fingerprintscan/ [45]
PANTHER http://www.pantherdb.org [46]
HAMAP http://hamap.expasy.org [47]
PIR http://pir.georgetown.edu [48]
TIGRFAM http://www.jcvi.org/cgi-bin/tigrfams/index.cgi [49]
InterPro http://www.ebi.ac.uk/interpro/ [50]
MetaCyc http://metacyc.org [51]
KEGG http://www.genome.jp/kegg/ [52]
SignalP http://www.cbs.dtu.dk/services/SignalP/ [53]
TMHMM http://www.cbs.dtu.dk/services/TMHMM/ [54]
Phobius http://phobius.sbc.su.se [55]
GeneOntology http://geneontology.org [56]
SQL Database
SQLite https://www.sqlite.org