DESCRIPTION OF THE FILE "proteocomp.html"

TAXONOMY USED

STRUCTURE OF THE FILE "proteocomp.html"

1. Prosite motifs ordered by family. For each motif, 2 plots representing the 42 proteomes compared ("plot42" and zoom42").
2. Exhaustive list of pairs of the 42 proteoms. For each pair, 2 plots ("plot2" and "plot2name")
3. Detailed comparisons. List of the 42 proteomes. For each proteom,
   1. list of comparison with the 41 other proteomes. For each comparison, access to "plot2" and "plot2name"
   2. exceptional motifs for the proteome. For each motif, access to "plot42" and "zoom42"

DESCRIPTION OF THE PLOTS

• "plot42" - Example. Plot of the statistical indicators gamma for all the proteomes considered and for one Prosite motif. The scale is shown at the top of the plot. This scale is independant of the motif. The two colums of the right respectively are, for the number of matches of the motif in the proteome, (left) the expectation in a random text of size of the proteome; (right) the observed count. The statistical parameters gamma are computed relative to normalized length of 1 million amino-acids for each proteome.
• "zoom42" - Example. Essentially the same as "plot42", but the horizontal scale has been stretched as much as possible. The scale depends of the motif.
• "plot2" - Example. Comparison of 2 proteomes, for all the considered motifs. A cross represent a motif in the plot. Coordinates refer to the gamma values for the motifs. The parameters gamma are computed relative to the effective length of the proteomes (see these lengths listed below)
• "plot2name" - Example Identical to "plot42", but the name of the motif is placed one millimeter right to the cross representing the motif.

LENGTH OF THE PROTEOMES

 
dros_mela =  6617803
caen_eleg =  7863058
sacc_cere =  2937205
arab_thal = 11304307
aero_pern =   638811
arch_fulg =   660832
meth_jann =   502362
meth_ther =   525164
pyro_abys =   535786
pyro_hori =   568584
halo_nrc1 =   624005
ther_acid =   453115
aqui_aeol =   488484
baci_halo =  1169204
baci_subt =  1218487
borr_burg =   352644
buch_aphi =   187023
camp_jeju =   503501
chla_muri =   324428
chla_pneu =   361707
chla_trac =   312118
dein_radi =   951455
esch_coli =  1373785
haem_infl =   526801
heli_2pyl =   491768
heli_Jpyl =   493049
lact_lact =   655989
myco_geni =   175729
myco_lepr =   520057
myco_pneu =   237930
myco_tube =  1317198
neis_mena =   582084
neis_menb =   573863
past_mult =   667675
pseu_aeru =  1856757
rick_prow =   279044
syne_cyan =  1027015
ther_mari =   582037
trep_pall =   349913
urea_urea =   227717
vibr_chol =  1156096
xyla_fast =   744437