publication "The Unique Peptidome"

[pdawyndt]

Interesting observations with respect to pancore publication:

• Clostridium botulinum: example of genomes that are so-called complete, but are not
• ???: example of incorrect taxonomic identification of genome
• Mycobacterium bovis, Rickettsia prowazekii (and other of this genus): clonal species with highly similar genomes (core =~= pan)
• species with large number of genomes:
  • bacillus (almost all species)
  • bifidobacterium (almost all species)
  • chlamidia (almost all species)
  • clostridium botulinum
  • escherichia coli (25): may be compared with Lukjancenko et al (2010)
  • haemophilus influenzae
  • helicobacter pylori
  • legionella pneumophila
  • rickettsia prowazekii

To illustrate the process of an in silico trypsin digest and successive identification of the peptides, we could show an illustration of a protein with peptides marked as regions and under each region show the lowest common ancestor of that peptide. The example should contain at least one species-specific peptide, at least one genus-specific peptide and a peptide that is less specific than genus-level. This could also be shown on Unipept in a separate protein page, that also shows a multiple alignment of the family the protein belongs to, as a cartoon with clickable regions of peptides that are conserved or non-conserved in the family. We would need to look for a website where we can find such a ready-made alignment for the protein family.

Original issue by @pdawyndt on Wed Apr 10 2013 at 17:32. Closed by @bmesuere on Sun Jan 24 2016 at 13:20.

[pdawyndt]

referenties:

• Ueda et al.
• peptidome application
• wiktionary definition
• human peptidome display

Original comment by @pdawyndt on Wed Oct 30 2013 at 10:02.