DRAM2’s Default Databases

CAMPER: —

Use the key name “camper” to select

Citation: CAMPER has no citeation and is in beta so you should not be using i

dbCAN: —

Use the key name “dbcan” to select

Citation: Y. Yin, X. Mao, J. Yang, X. Chen, F. Mao, and Y. Xu, “dbcan: a web

resource for automated carbohydrate-active enzyme annotation,” Nucleic acids rese arch, vol. 40, no. W1, pp. W445–W451, 2012.

Genome_stats: —

Use the key name “stats” to select

Citation: This kit is used to get genome stats produced by prodigal

KEGG: —

Use the key name “kegg” to select

Citation: M. Kanehisa, M. Furumichi, Y. Sato, M. Ishiguro-Watanabe, and M. T

anabe, “Kegg: integrating viruses and cellular organisms,” Nucleic acids research , vol. 49, no. D1, pp. D545–D551, 2021.

KOfam: —

Use the key name “kofam” to select

Citation: T. Aramaki, R. Blanc-Mathieu, H. Endo, K. Ohkubo, M. Kanehisa, S. G

oto, and H. Ogata, “Kofamkoala: Kegg ortholog assignment based on profile hmm and

adaptive score threshold,” Bioinformatics, vol. 36, no. 7, pp. 2251–2252, 2020.

Methyl: —

Use the key name “methyl” to select

Citation: Methyl is a in hous db mostly make by McKayla Borton

Heme Regulatory Motifs Counts: —

Use the key name “heme” to select

Citation: This database is so simple “(C..CH)” it dose not warrant a citation

.

Peptidase: —

Use the key name “peptidase” to select

Citation: N. D. Rawlings, A. J. Barrett, P. D. Thomas, X. Huang, A. Bateman,

and R. D. Finn, “The merops database of proteolytic enzymes, their substrates and

inhibitors in 2017 and a comparison with peptidases in the panther database,” Nu

cleic acids research, vol. 46, no. D1, pp. D624–D632, 2018.

Pfam: —

Use the key name “pfam” to select

Citation: J. Mistry, S. Chuguransky, L. Williams, M. Qureshi, G. A. Salazar,

E. L. Sonnhammer, S. C. Tosatto, L. Paladin, S. Raj, L. J. Richardson et al., “Pf am: The protein families database in 2021,” Nucleic acids research, vol. 49, no. D1, pp. D412–D419, 2021.

Sulfur: —

Use the key name “sulfur” to select

Citation: Li W, O’Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, C

oulouris G, Chitsaz F, Derbyshire MK, Durkin AS, Gonzales NR, Gwadz M, Lanczycki CJ, Song JS, Thanki N, Wang J, Yamashita RA, Yang M, Zheng C, Marchler-Bauer A, T hibaud-Nissen F. RefSeq: expanding the Prokaryotic Genome Annotation Pipeline rea ch with protein family model curation. Nucleic Acids Res. 2021 Jan 8;49(D1):D1020 -D1028. doi: 10.1093/nar/gkaa1105. PMID: 33270901; PMCID: PMC7779008.

UniRef: —

Use the key name “uniref” to select

Citation: Y. Wang, Q. Wang, H. Huang, W. Huang, Y. Chen, P. B. McGarvey, C. H

. Wu, C. N. Arighi, and U. Consortium, “A crowdsourcing open platform for literat