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How To Derive Pan Proteome

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

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updated by Biostar Biostar • written by Naren Naren

2 answers

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.

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updated by Ram Ram • written by Neilfws Neilfws

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/]

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written by Naren Naren

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

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written by bob-lowlow • bob-lowlow

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

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written by Neilfws Neilfws

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

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written by Naren Naren

@geargalr: it took 35 mins for a genome .

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written by Naren Naren

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