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era7 bioinformatics R&D group

Automatic annotation of E. coli H112180280 strain (sequence and assembly by HPA)

And right now we’ve finished the automatic annotation of the assembly of new strain that HPA (Health Protection Agency UK)  made available yesterday (get the assembly file here http://www.hpa-bioinformatics.org.uk/lgp/resource/454Scaffolds.fna)

Once more we’ve used BG7 and the same set of reference proteins (137,063 proteins in total):

  • 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 5,916 genes

  • 5,792 protein encoding genes
  • 124 RNA genes

4,912 out of the 5,792 (84.80%) protein encoding genes have canonical start and stop codon and haven´t either frame-shifts or intragenic stop codons.

615 out of the 5,792 (10.61%) 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/H112180280/seqProject/HealthProtectionAgencyUK/annotations/era7bioinformatics/era7_HPA_H112180280_annotations)