Representative Proteomes (RP) ============================= Representative Proteomes are proteomes that can best represent all complete proteomes in terms of the majority of the sequence space and information. We provide four sets of Representative Proteomes based on co-membership threshold (CMT) cut-off to allow users to decrease or increase the granularity of the sequence space based on their requirements (PMID: 21556138, http://pir.georgetown.edu/rps/). This directory contains an archive sub-directory, a rg sub-directory and the following files: 1) readme.txt: This file; 2) release_note.txt: current release note; 3) summary.html: Summary statistics for the RPs; 4) completeProteomeSet-seqs.fasta.gz: sequence file for all complete proteomes (one protein per gene); 5) rp-seq-x.fasta.gz, (x=15, 35, 55, 75): RP sequence files at different CMT cut-offs; 6) rpg-x.txt (x=15, 35, 55, 75): Text files of Representative Proteomes Group (RPG) at different CMT cut-offs; Note: rpg-x.txt file format: >rp_UPID taxon_id organism_code name taxon_group_id score(PPS:IsRefP,IsRP,#PMID,MeanAS,#Entry) C(CUTOFF) RefP X_to_seed(X) UPID tax_id organism_code name taxon_group_id score(PPS:IsRefP,IsRP,#PMID,MeanAS,#Entry) X_to_rp(X) RefP X_to_seed(X) ... (terms are separated by a tab) Example: >UP000000757 246196 MYCS2 Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis) Bac/ActnBac 37114.05014(PPS:1,1,311,13.52,6583) 55(CUTOFF) RefP 93.81943(X-seed) UP000006158 246196 MYCS2 Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis) Bac/ActnBac 19114.01223(PPS:0,0,295,13.75,6565) 92.92361(X-RP) 93.77106(X-seed) UP000011200 1214915 MYCSE Mycolicibacterium smegmatis (strain MKD8) (Mycobacterium smegmatis) Bac/ActnBac 19108.23869(PPS:0,0,1,10.62,6732) 85.71871(X-RP) 88.52866(X-seed) UP000062255 134601 MYCGD Mycobacterium goodii (Mycolicibacterium goodii) Bac/ActnBac 27108.80251(PPS:0,1,2,11.42,6298) 70.29742(X-RP) 71.41830(X-seed) UP000255288 1772 MYCSM Mycolicibacterium smegmatis (Mycobacterium smegmatis) Bac/ActnBac 19110.47150(PPS:0,0,42,13.12,6579) 93.81943(X-RP) 100.00000(X-seed) Home page: http://pir.georgetown.edu/rps/ Browse: http://pir.georgetown.edu/rps/browse.html BLAST search: http://pir.georgetown.edu/rps/blast_rp.shtml Make your own RP sequence file: http://pir.georgetown.edu/rps/mk_rp.shtml FTP download: ftp://ftp.pir.georgetown.edu/databases/rps/ Sequence files at different cut-offs and for all complete proteomes (one protein per gene). Text files of proteome clusters at different co-membership threshold cut-offs. ftp://ftp.pir.georgetown.edu/databases/rps/rg Text files of genome clusters at different co-membership threshold cut-offs. Representative genomes (RGs) are constructed based on the corresponding RPs. ------------------------------------ Protein Information Resource (PIR) Georgetown University Medical Center 3300 Whitehaven Street, NW, Suite 1200 Washington, DC 20007, USA Email: pirmail@georgetown.edu