Era7 e. coli TY2482 annotation with bg7 system
- who Raquel Tobes from Oh no sequences! (Era7)
- what automatic annotation of E. coli TY-2482 genome (see Nick Loman assembly at assemblies) with [BG7 system] (http://www.slideshare.net/marina_manrique/bg7-a-new-system-for-bacterial-genome-annotation-designed-for-ngs-data)
- date 3-Jun-2011
BG7 system developed by Oh no sequences! was used to get this annotation.
BG7 pipeline is a pipeline specially designed to handle data from NGS. One of the most important features of the pipeline is that we predict ORF searching for protein similarity. So we start with a search of the reference proteins in the contigs and then we define the ORF. We preserve all the CDS found (although they haven't canonical start or stop codons and although they have frameshifts or intrastop codon) so the system is pretty robust to NGS errors that may cause the lose of start/stop signals or changes in the frameshit.
These are the datasets we used in the annotation
Nick Loman's assembly of the 5x314 IonTorrent chips published by BGI (2-Jun-2011)
We took as reference proteins a set of 137,063 proteins. This set includes:
- The representative Uniprot proteins corresponding to all Uniref90 clusters for all Escherichia coli proteins
- All Uniprot proteins from organisms including in their name the terms “EHEC” or “EAEC”
- All Uniprot proteins from bacteria that have in any Uniprot field the term “toxin”
- All Uniprot proteins from bacteria that have in any Uniprot field “hemolysin”
- All the proteins from Salmonella typhi, Yersinia pestis and Shigella dysenteriae
You can get the files of the results of this annotation from the repo here: https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/tree/master/strains/TY2482/seqProject/BGI/annotations/era7bioinformatics
We have predicted 6,327 genes
- 6,156 protein encoding genes
- 171 RNA genes (rRNA and tRNA)
1,326 out of the 6,156 protein encoding genes have canonical start and stop codon and haven´t either frame-shifts or intragenic stop codons.
2,479 out of the 6,156 protein encoding genes have some frameshifts or intragenic stop codon in their sequences, probably caused by inherent technology errors. However, our system is tolerant to errors of massive sequencing technologies and it has been able to detect this rich set of genes even with very preliminary sequencing results.
Probably some of the proteins detected are fragmented and could appear as two different predicted genes if they are at the end of different contigs.
We have analyzed the taxonomic origin of the proteins responsible for the prediction of the detected genes. Figure 1 shows the result of this analysis.
A detailed list with the taxonomic origin of all the proteins detected in E. coli TY-2482 can be found in the Table 1 of this post