Integrated proteogenomics database

Bacteria iconB. henselae MQB277_tryptic

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.
iPtgxDB Release Info
Versions

Version

1
Versions

Date

09.11.2016

Downloads icon Downloads

Compression icon

TAR.GZ

File icon

Size

2.9 MB
Data icon

MD5

c92051ade39f74b085fd5fc954c70ecc
Data icon

SHA1

58f80fa55823a07c1fa927bfcf257c6d553446eb
Compression icon

ZIP

File icon

Size

3.0 MB
Data icon

MD5

e96f6a0bebe6a289b2ebfed629954710
Data icon

SHA1

ed70edadd6f7e42250d3e7eaf48986e86be61d69