B. henselae Houston-1

Bartonella henselae strain ATCC49882 (Houston-1; Genbank #NC_005956), isolated from an HIV-positive patient, is the reference strain [1].

An iPtgxDB was created by hierarchically integrating protein coding sequences from these annotation resources:

Hierarchy	Resource	Link
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 [2]	v2.7.3, accessed 03/09/2016
5	Prodigal [3]	Ab initio gene predictions from Prodigal (v2.6)
6	ChemGenome [4]	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.

References

1. Alsmark, C.M., Frank, A.C., Karlberg, E.O., Legault, B.A., Ardell, D.H., Canback, B., Eriksson, A.S., Naslund, A.K., Handley, S.A., Huvet, M. et al. 2004. The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae. Proc Natl Acad Sci U S A 101: 9716-9721.
2. Vallenet, D., Belda, E., Calteau, A., Cruveiller, S., Engelen, S., Lajus, A., Le Fevre, F., Longin, C., Mornico, D., Roche, D. et al. 2013. MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res 41: D636-647.
3. Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W., and Hauser, L.J. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
4. Singhal, P., Jayaram, B., Dixit, S.B., and Beveridge, D.L. 2008. Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations. Biophys J 94: 4173-4183.
5. Omasits, U., Varadarajan, A. R., Schmid, M., Goetze, S., Melidis, D., Bourqui, M., Nikolayeva, O., Quebatte, M., Patrignani, A., Dehio, C., Frey, J. E., Robinson, M. D., Wollscheid, B., and Ahrens., C. H. An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. bioRxiv, Cold Spring Harbor Labs Journals, 2017.