Tables Comparing the Various Genomes

Table Name Size (kb), Format Links Fields (keys bold) Description
tm report 1 k, tab delim. data, head binnam_, from, to, ibin, PS, SC, MJ, HI, MP, MG, EC, SS, HP 

Histogram of TM elements
For genomes PS SC MJ HI MP MG EC SS HP
Using the following histogram parameters
binmax = 20.5, binmin = -0.5, binsize = 1
tbl_name (in) = id_ntm
minscop sol 173 k, fasta data, head did_, seq 

This fasta file contains the sequences in pdb95d-1.35
which correspond to scop classes 123457
and which are in Ted's minscop
len report 2 k, tab delim. data, head binnam_, from, to, ibin, SC, MJ, HI, MP, MG, EC, SS, HP, TP, PS, PA, PB, PM, PC, BP 

Histogram of sequence lengths
For genomes SC MJ HI MP MG EC SS HP TP PS PA PB PM PC BP
Using the following histogram parameters
binmax = 1000, binmin = 0, binsize = 33.3333333
tbl_name (in) = full_len_segs
did year 29 k, tab delim. data, head did_, fidfam, year 

This file contains the identifiers in minscop
with the scop family fid next to each id 
and the year of the oldest pdb in the in family
according to the scop page
file:///Y|/a/2/pdbgen/ted/date/fad.all.html
Ted did this.
biophys prots 6 k, tab delim. data, head did_, PDB, Select, length, class, name, fid, seq 

This file contains a list of biophysical proteins, which
is edited from Lynne Regan's original list.
comp report 200 k, tab delim. data, head selection, genome, sum, total_seqs, masked_seqs, total_chars, masked_chars, total_segs, masking_segs, mask_chars_per_seg, mask_chars_per_seq, frac_masked_chars, frac_masked_seqs, masking_segs_per_seq, dav_rms, dps_rms, dav_A, dav_C, dav_D, dav_E, dav_F, dav_G, dav_H, dav_I, dav_K, dav_L, dav_M, dav_N, dav_P, dav_Q, dav_R, dav_S, dav_T, dav_V, dav_W, dav_Y, dps_A, dps_C, dps_D, dps_E, dps_F, dps_G, dps_H, dps_I, dps_K, dps_L, dps_M, dps_N, dps_P, dps_Q, dps_R, dps_S, dps_T, dps_V, dps_W, dps_Y, pct_A, pct_C, pct_D, pct_E, pct_F, pct_G, pct_H, pct_I, pct_K, pct_L, pct_M, pct_N, pct_P, pct_Q, pct_R, pct_S, pct_T, pct_V, pct_W, pct_Y, A_n, C_n, D_n, E_n, F_n, G_n, H_n, I_n, K_n, L_n, M_n, N_n, P_n, Q_n, R_n, S_n, T_n, V_n, W_n, Y_n, 0_n, 1_n, 2_n, 3_n, 4_n, 5_n, 6_n, 7_n, 8_n, 9_n, selections_long, sort 

Report on the compositions in the genomes
PS EC HI HP MG MJ MP SC SS TP AV SD
based on the following a.a. selections 
seq pdb lcl tms lnk alp bet ucd cdo gor otm olc 
(version 3)
descrip did 493 k, tab delim. data, head id_, bestrep, N_minsp, N_scop, objname 

This table describes the various sequence family-level objects in
scop. Each scop domain identifier is described by a name and by
whether or not it is included in minscop.
An id number is given as the key.
bestrep  = a best representative (scop domain id)
N_minsp  = the number in minscop
N_scop   = the number in all of scop (1.35)
objname  = the name for objects from dir.lin.scop.txt
descrip fold 22 k, tab delim. data, head id_, bestrep, N_minsp, N_scop, objname 

This table describes the various fold-level objects in scop. 
An id number is given as the key.
bestrep  = a best representative (scop domain id)
N_minsp  = the number in minscop
N_scop   = the number in all of scop (1.35)
objname  = the name for objects from dir.lin.scop.txt
descrip sfam 32 k, tab delim. data, head id_, bestrep, N_minsp, N_scop, objname 

This table describes the various superfamily-level objects in scop. 
An id number is given as the key.
bestrep  = a best representative (scop domain id)
N_minsp  = the number in minscop
N_scop   = the number in all of scop (1.35)
objname  = the name for objects from dir.lin.scop.txt
did fids 245 k, tab delim. data, head
did fids135 36 k, tab delim. data, head did_, fids 

fids for each of the proteins in pdb40d
did fids minscop 30 k, tab delim. data, head did_, fids 

fids for each of the proteins in minscop
did pdbsel 188 k, tab delim. data, head did_, pdb, sel 

List of each domain id scop (did) with the pdb id and residue
selection that it corresponds to.
fa out link 01 2195 k, tab delim. data, head score, start1, stop1, start2, stop2, ident, clust
fid12 fold 14 k, tab delim. data, head
fid year 16 k, tab delim. data, head
fix fold names 3 k, tab delim. data, head
len report MODES 1 k, tab delim. data, head genome, binnam_, from, to, ibin 

Mode (top value in histogram sequence lengths) for each genome.
For genomes SC MJ HI MP MG EC SS HP TP PS PA PB PM PC BP
Using the following histogram parameters
binmax = 1000, binmin = 0, binsize = 33.3333333
tbl_name (in) = full_len_segs
pdb100d 135 2455 k, Hidden data, head - 

-
pdb40d-1.35 298 k, fasta data, head
pdb40d135 sol 202 k, Hidden data, head - 

-
pdb95d 135 533 k, Hidden data, head - 

-
scop135 dirdom 420 k, tab delim. data, head
tm len report 2 k, tab delim. data, head binnam_, from, to, ibin, SC, MJ, HI, MP, MG, EC, SS, HP, TP 

Histogram of tm seg lengths
For genomes SC MJ HI MP MG EC SS HP TP
Using the following histogram parameters
binmax = 60.5, binmin = 19.5, binsize = 1
tbl_name (in) = tm_segs
tm report MODES 1 k, tab delim. data, head genome, binnam_, from, to, ibin 

Mode (top value in histogram TM elements) for each genome.
For genomes PS SC MJ HI MP MG EC SS HP
Using the following histogram parameters
binmax = 20.5, binmin = -0.5, binsize = 1
tbl_name (in) = id_ntm
top10 summary 11 k, tab delim. data, head fid12_, all3_i, avg_frac_f, count{MJ}, count{HI}, count{SC}, frac{MJ}, frac{HI}, frac{SC}, name 

  out->store(,,
	      ,,,
	      ,,,
	      );
when all struc report 19 k, tab delim. data, head year, stat, pdb-AV, pdb-SC, pdb-MJ, pdb-HI, pdb-MP, pdb-MG, pdb-EC, pdb-SS, pdb-HP, ucd-AV, ucd-SC, ucd-MJ, ucd-HI, ucd-MP, ucd-MG, ucd-EC, ucd-SS, ucd-HP, value 

Report on what fraction of the genome remains
uncharacterized structurally. Based 
on the following genomes
SC MJ HI MP MG EC SS HP
and the following selections
pdb ucd

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