How To Derive Pan Proteome

Question

[Naren]

How to derive pan proteome of 28 microbial species?
I already have core genes / orthologs between all the species.
I also have unique genes of all species.
I only had problem with getting accessory genes/ proteins.
I am not willing to do blast 784 times.
help pls

Answer 1

[Neilfws]

First, pan-proteome is not a widely-used term, nor is it very well defined. I assume you mean it in the sense used in this article:

core (found in all) + accessory (found in > 2) + unique (found in 1)

I don't think the 3 sets together are interesting or useful ; pan-proteome is just a term used to describe those 3 sets.

Second, why are you "not willing" to run 784 BLAST searches? Perhaps you mean "not able"? If you're able but not willing, perhaps consider another career ;)

Third, BLAST is not necessarily the best tool. You may find it more useful to cluster the protein sequences using e.g. CD-HIT. In fact, the output from that may come close to giving you the groupings that you need.

[Naren]

Thanks @Neilfws: I am a naive to the field (specifically bacterial genomics). I am able to do Blast whatever times it needs. but I wanted some smarter way. that`s what I meant. I want this as a career.:) I saw a paper in which they compared cog distribution in core and pan genomes of some set of species. I wanted to do that for different set of species.And pan genome is considered to be useful in vaccine design against pathogenic strains. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752168/]

Answer 2

[bob-lowlow]

I don't really understand what you mean? How will 784 blasts give you the pan proteome? but if you want to save on blasting stuff, assuming you have amino acid sequence information, you can use this http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi it's essentially batch blasting

[Neilfws]

I assume they mean that all-versus-all BLAST for 28 species = 28 x 28 = 784.

[Naren]

Thanks, for replying, @feargalr I think Neilfws made it clear.

[Naren]

@geargalr: it took 35 mins for a genome .