Sinorhizobium meliloti strain 2011 (Genbank #NC_020528 is the reference strain [1] which includes two plasmids #NC_020527 and #NC_020560.
An iPtgxDB was created by hierarchically integrating protein coding sequences from three annotation resources (1-3) and three predictions:
Hierarchy | Resource | Link |
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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 | 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) |
6 | in silico ORFs | The in silico ORF annotations were generated as described by Omasits and Varadarajan et al., 2017 [5] |
Only ORFs above a selectable length threshold (here 18 aa) were considered. The iPtgxDB was created using the hierarchy RefSeq > Genbank > Genoscope > Prodigal > ChemGenome > in silico. Files were parsed to extract the identifier, coordinates and sequences of bona fide protein-coding sequences (CDS) and pseudogene entries. For more detail on how we generate iPtgxDBs and how the identifiers can be interpreted, please see reference [5].
iPtgxDB Release Info | |
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![]() Version |
1 |
![]() Date |
19.09.2019 |