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

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]

Muscle

http://www.drive5.com/muscle

[29]

Kalign

http://www.ebi.ac.uk/Tools/msa/kalign

[32]

Phylip

http://evolution.gs.washington.edu/phylip

[33]

Markov chain Clustering (MCL)

http://micans.org/mcl

[28]

EMOSS

http://emboss.sourceforge.net

[20]

InterProScan

https://code.google.com/p/interproscan/

[40]

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]

SQLite

https://www.sqlite.org