How to download proteins in my scenario?

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3.9 years ago

Bioinfo_learner ▴ 40

I have editted my question on the basis of answers given for further clarification. I am aware of Uniprot proteomes. My specific questions are: 1)Does it matter in the downstream analysis of proteome if the strain is scaffold level assembled or completely assembled? My downstream analysis requires Blastp, clustering, phylogeny and GO ontologies. 2) I could not find the geographical location/origin of strains and proteomes in PlasmoDB database.

Regards.

proteins blast+ sequencing Assembly genome • 760 views

ADD COMMENT • link 3.8 years ago by Bioinfo_learner ▴ 40

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Get the proteomes for these from UniProt.

ADD REPLY • link 3.9 years ago by GenoMax 141k

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I do know where I can get the proteomes from but how do I know if these are complete? Also if you read my questions, I have little doubts about how my dataset is fine or not.

ADD REPLY • link 3.9 years ago by Bioinfo_learner ▴ 40

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how do I know if these are complete?

No proteme is likely complete since we don't have a catalog of every protein that is expressed in the lifecycle of an organism. UniProt proteomes have a BUSCO estimate of how complete the proteome is. That should give you a rough idea of how complete the proteome is.

ADD REPLY • link 3.9 years ago by GenoMax 141k

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