# *Bartonella henselae* MQB277

| iPtgxDB Release     ||
| ------: | :--------: |
| Version | 1          |
| Date    | 09.11.2016 |

## Downloaded from
[/database/annotations/b-henselae-mqb277](/database/annotations/b-henselae-mqb277)

*Bartonella henselae* strain MQB277 is a laboratory strain derived from CHDE101. It harbors a deletion of the response regulator batR (BH00620) and its cognate sensor histidine kinase batS (BH00610), and a chromosomal integration of PbepD:gfpmut2.

An iPtgxDB was created for this lab strain by hierarchically integrating protein coding sequences from the *ab initio* gene prediction software Prodigal (Hyatt et al. 2010) (v2.6) and *in silico* ORFs on top.

| Hierarchy | Resource | Link |
| :---: | :--- | :--- |
| 1 | Prodigal [2] | *Ab initio* gene prediction from Prodigal (v2.6) |
| 2 | *in silico* ORFs | *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 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. Omasits, U., Quebatte, M., Stekhoven, D.J., Fortes, C., Roschitzki, B., Robinson, M.D., Dehio, C., and Ahrens, C.H. 2013. Directed shotgun proteomics guided by saturated RNA-Seq identifies a complete expressed prokaryotic proteome. Genome Research 23: 1916-1927.
2. 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.
3. 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.
