Sinorhizobium meliloti strain 2011 (Genbank #NC_020528) is the reference strain .
An iPtgxDB was created by hierarchically integrating protein coding sequences from three these annotation resources (1-3) and three predictions:
|1||NCBI RefSeq||GCF_000346065.1_ASM34606v1; from 19/05/2017|
|2||NCBI Genbank||GCA_000346065.1_ASM34606v1; from 31/01/2014|
|3||Genoscope ||v2.7.3, accessed 14/11/2018|
|4||Prodigal ||Ab initio gene predictions from Prodigal (v2.6)|
|5||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)|
|6||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 > Genbank > Genoscope > ChemGenome > Prodigal > in silico. Files were parsed to extract the identifier, coordinates and sequences of bona fide protein-coding sequences (CDS) and pseudogene entries. For more detail on how we generate iPtgxDBs and how the identifiers can be interpreted, please see reference .
|iPtgxDB Release Info|