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Protein Database Downloader (version 0.3.4)

Download from:

Select database source. cRAP acts as a database for common MS contaminants. UniProtKB is a cross species collection of functional protein databases

Taxonomy:

select species for protein database

taxon_id:

Specify a NCBI taxon id to override species selection

reviewed:

UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database- may contain redundant sequences, but there is a higher chance peptides will be identified. UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database- less of a chance peptides will be identified but less sequence redundancy

Proteome Set:

Include isoform data:

several different forms of a given protein are incorporated into database

Output

Creates a FASTA file of specified protein sequences for comparison with experimental MS/MS data in search algorithm.

External Links

Galaxy-P_101 shows usage Protein Database Downloader tool in the creation of a workflow

UniProtKB provides additional information about the UniProt Knowledgebase

Additional Protein Fasta URLs

HUMAN GUT METAPROTEOME:

61MB gzip http://www.bork.embl.de/~arumugam/Qin_et_al_2010/frequent_microbe_proteins.fasta.gz

MOUSE GUT MICROBIOTA:

See: http://gigadb.org/dataset/view/id/100114/token/mZlMYJIF04LshpgP