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era7 bioinformatics R&D group

Automatic annotation of E. coli LB226692 genome

And this morning we’ve finished the automatic annotation of the other isolate from the outbreak whose sequence is also available. The isolate LB226692.

Life Tech and University of Muenster have sequenced the genome and done a hybrid mapping assembly getting finally 364 contigs. More details on the assembly method here

We usedBG7 system to annotate the genome.

In this case we’ve selected as reference protein the same protein set we used to annotate the other E. coli isolate (the TY-2482). This protein set has 137,063 proteins and 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

Results

We’ve detected 6,302 genes

  • 6,132 protein encoding genes
  • 170 RNA genes

4,504 out of the 6,132 (73.45%) protein encoding genes have canonical start and stop codon and haven´t either frame-shifts or intragenic stop codons.

1,125 out of the 6,132 (18.34%) protein encoding genes have some frameshifts or intragenic stop codon in their sequences, probably caused by inherent technology errors.

You can get the results of the annotation here https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/tree/master/strains/LB226692/annotations/era7bioinformatics