Bartonella henselae strain ATCC49882 (Houston-1; Genbank #NC_005956), isolated from an HIV-positive patient, is the reference strain .
An iPtgxDB was created by hierarchically integrating protein coding sequences from these annotation resources:
|1||NCBI RefSeq 2015||GCA_000046705.1_ASM4670v1; from 07/30/2015|
|2||NCBI RefSeq 2013||Bartonella_henselae_Houston_1_uid57745; from 06/10/2013|
|3||Ensembl||Ensembl's Genomes project (GCA_000046705.1, Feb/2015)|
|4||Genoscope ||v2.7.3, accessed 03/09/2016|
|5||Prodigal ||Ab initio gene predictions from Prodigal (v2.6)|
|6||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)|
|7||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 2015 > RefSeq 2013 > Ensembl > 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.
|iPtgxDB Release Info|