This is the parental strain (Genbank #CP009273) of the widely used Escherichia coli Keio gene knockout collection .
An iPtgxDB was created by hierarchically integrating protein coding sequences from the following annotation resources:
|1||NCBI RefSeq||CP009273.1; from 30/10/2014|
|2||IMG ||Integrated Microbial Genomes (IMG) initiative of the Joint Genome Institute (JGI); Ga0058822, from 12/08/2014|
|3||Prodigal ||Ab initio gene predictions from Prodigal (v2.6)|
|4||ChemGenome ||Ab initio gene predictions from ChemGenome (v2.0, http://www.scfbio-iitd.res.in/chemgenome/chemgenomenew.jsp; with parameters: method, Swissprot space; length threshold, 70 nt; initiation codons, ATG, CTG, TTG, GTG)|
|5||in silico ORFs||The in silico ORF annotations were generated as described by Omasits and Varadarajan et al., 2017|
Only ORFs above a selectable length threshold (here 18 aa) were considered. The iPtgxDB was created using the hierarchy RefSeq > JGI > Prodigal > ChemGenome > in silico. Files were parsed to extract the identifier, coordinates and sequences of bona fide protein-coding sequences (CDS) and pseudogene entries.
|iPtgxDB Release Info|