Integrated proteogenomics database

Bacteria iconS. meliloti 2011_undigested_custom

Sinorhizobium meliloti strain 2011 (Genbank #NC_020528 is the reference strain [1] which includes two plasmids #NC_020527 and #NC_020560.

A small custom iPtgxDB was created by hierarchically integrating protein coding sequences from three annotation resources (1-3) and two predictions:

Hierarchy Resource Link
1 NCBI RefSeq GCF_000346065.1_ASM34606v1; from 19/05/2017
2 NCBI Genbank GCA_000346065.1_ASM34606v1; from 31/01/2014
3 Genoscope [2] v2.7.3, accessed 14/11/2018
4 Prodigal [3] Ab initio gene predictions from Prodigal (v2.6)
5 276 RiboSeq predictions The RiboSeq candidates were selected as described by Hadjeras et al., 2022 [4]

Only ORFs above a selectable length threshold (here 18 aa) were considered. The iPtgxDB was created using the hierarchy RefSeq > Genbank > Genoscope > Prodigal > RiboSeq. Files were parsed to extract the identifier, coordinates and sequences of bona fide protein-coding sequences (CDS) and pseudogene entries. For extensions or reductions to already annotated CDSs, the full sequence was included, allowing to identify such proteins using the proteomics data obtained from undigested samples. For more detail on how we generate iPtgxDBs and how the identifiers can be interpreted, please see reference [5].

References

  1. Sallet, E., Roux, B., Sauviac, L., Jardinaud, M. F., Carrere, S., Faraut, T., de Carvalho-Niebel, F., Gouzy, J., Gamas, P., Capela, D., Bruand, C. and Schiex, T. 2013. Next-generation annotation of prokaryotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011. DNA Res 20(4): 339-354.
  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. Hadjeras, L., Heiniger, B., Maaß, S., Scheuer, R., Gelhausen, R., Azarderakhsh, S., Barth-Weber, S., Backofen, R., Becher, D., Ahrens, C.H., Sharma, C.M., Evguenieva-Hackenberg, E. 2022. Small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti. bioRxiv 2022.11.12.516264
  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. 2017. An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. Genome Research. 27: 2083-2095.
iPtgxDB Release Info
Versions

Version

1
Versions

Date

02.02.2022

Downloads icon Downloads

Compression icon

TAR.GZ

File icon

Size

1.8 MB
Data icon

MD5

146c5fce8fc703eb5a09aa76c2b2e589
Data icon

SHA1

d0012f5dc4723ce2aa2dfe3b069070189f58762f
Compression icon

ZIP

File icon

Size

1.9 MB
Data icon

MD5

0ba762a68ef064aa1f05b6dd9636097a
Data icon

SHA1

958589f6e56706d278ca46733bcb80ca10ff9e48