Pathways

Post-analysis categorization
- Literature search
Post-survey categorization
- Features validated in most cases
- Features not validated
Simple lists
Preliminary lists

Tool name

The SEED

URL

http://theseed.uchicago.edu/FIG/index.cgi

Important features

Annotation and analysis tool for microbial genomes.

Citations

Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Cr\E9cy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A,Portnoy V, Pusch GD, Rodionov DA, RFCckert C, Steiner J, Stevens R, Thiele I,Vassieva O, Ye Y, Zagnitko O, Vonstein V. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. Print 2005. PubMed PMID: 16214803; PubMed Central PMCID: PMC1251668.

Year of publication

2005

Rank by usage frequency

100

Comments

Function

Pathways in yeast, Pathways in bacteria, Pathways in E. coli, Pathways in virus, Metabolic pathways, Pathways with their evolutionary relationships, Pathways collected from multiple pathway resources, Graphical representation of pathways