Help: Prokaryotic background models

Overview

1. Calculation of the higher order background models
2. Statistics
3. References

Calculation of the higher order background models
All GenBank files corresponding to the listed accessionnumbers where downloaded. Intergenic regions were delineated according to the modules of INCLUSive (Thijs et al., 2002). Based on these intergenics higher order background models were calculated. Therefore, the frequency of all oligonucleotides of order m and m+1 are counted to generated resp. the frequency table of all oligonucleotides and the transition matrix of the background model. The transition matrix stores the probability of a nucleotide given the m previous nucleotides in the sequence. The following table shows part of the third-order background model based on the intergenic sequences in Escherichia coli (K12). The first element in the matrix thus represents the probability of finding an A in the intergenics of E.coli given the fact that there are three preceding A's.

Content	A	C	G	T
AAA	0.3788	0.1715	0.1655	0.2842
AAC	0.3530	0.2052	0.2405	0.2014
AAG	0.2678	0.2447	0.2461	0.2414
AAT	0.3142	0.2007	0.2009	0.2842
ACA	0.3625	0.1596	0.2208	0.2571
...	...	...	...	...
TTC	0.3325	0.2136	0.1680	0.2859
TTG	0.2333	0.3207	0.1180	0.3279
TTT	0.2301	0.1907	0.1801	0.3992

Overview of the computed models
The table below gives the accession numbers for which a background model was calculated, the description of the accession number and the single nucleotide frequency of the intergenic sequences. Remark at first that for Vibrio cholerae, Brucella melitensis and Deinococcus radiodurans, the intergenic sequences of both chromosomes were combined to calculate a single genome background model. Secondly, it should be noted that for genomes and plasmids separate background models were calculated.

Accession Number	Description of the organism	Single Nucleotide Frequency A C G T
NC_000854	Aeropyrum pernix	0.241861	0.255022	0.260723	0.242394
NC_002147	Agrobacterium tumefaciens (plasmid pTi-SAKURA)	0.240459	0.259457	0.26361	0.236475
NC_003306	Agrobacterium tumefaciens (C58 Dupont plasmid AT)	0.245357	0.258775	0.261389	0.234479
NC_003304	Agrobacterium tumefaciens (C58 U.Wash circular chromosome)	0.242733	0.26016	0.26263	0.234478
NC_003305	Agrobacterium tumefaciens (C58 U.Wash linear chromosome)	0.243302	0.258823	0.261405	0.23647
NC_003062	Agrobacterium tumefaciens (C58 circular chromosome)	0.243589	0.259362	0.258827	0.238222
NC_003063	Agrobacterium tumefaciens (C58 linear chromosome)	0.245508	0.259408	0.257901	0.237183
NC_003064	Agrobacterium tumefaciens (C58 plasmid AT)	0.243119	0.259851	0.262967	0.234063
NC_003065	Agrobacterium tumefaciens (C58 plasmid Ti)	0.263051	0.239196	0.241812	0.255941
NC_000918	Aquifex aeolicus	0.30665	0.194991	0.204513	0.293847
NC_000917	Archaeoglobus fulgidus	0.317611	0.180168	0.187041	0.315179
NC_003995	Bacillus anthracis (A2012)	0.359211	0.131324	0.169541	0.339925
NC_001496	Bacillus anthracis (virulence plasmid PX01)	0.361732	0.141994	0.161688	0.334586
NC_002570	Bacillus halodurans	0.319638	0.172334	0.207455	0.300574
NC_000964	Bacillus subtilis	0.328008	0.167476	0.193845	0.310671
NC_003278	Bacteriophage phi CTX	0.190154	0.339068	0.308041	0.162737
NC_001318	Borrelia burgdorferi	0.395511	0.089595	0.11843	0.396465
NC_002528	Buchnera sp. (APS)	0.4282	0.077825	0.081557	0.412418
NC_002163	Campylobacter jejuni	0.396611	0.102881	0.1212	0.379308
NC_002696	Caulobacter crescentus	0.193431	0.30843	0.30567	0.192469
NC_002620	Chlamydia muridarum	0.321674	0.166279	0.177119	0.334928
NC_002179	Chlamydia pneumoniae (AR39)	0.333693	0.160117	0.160409	0.345781
NC_000117	Chlamydia trachomatis	0.313897	0.172219	0.183978	0.329906
NC_000922	Chlamydophila pneumoniae (CWL029)	0.328908	0.165686	0.167276	0.33813
NC_003030	Clostridium acetobutylicum (ATCC824)	0.382556	0.109831	0.153613	0.354
NC_003366	Clostridium perfringens	0.408966	0.080243	0.124114	0.386676
NC_001895	Enterobacteria phage (P2)	0.296663	0.220681	0.21143	0.271226
NC_002371	Enterobacteria phage (P22)	0.298211	0.217804	0.217362	0.266622
NC_000913	Escherichia coli (K12)	0.295326	0.205887	0.20227	0.296517
NC_002655	Escherichia coli (O157:H7 EDL933)	0.295658	0.204987	0.206437	0.292918
NC_002695	Escherichia coli (O157:H7)	0.295608	0.204037	0.20508	0.295275
NC_002142	Escherichia coli (plasmid pB171)	0.284904	0.217931	0.219671	0.277494
NC_002525	Escherichia coli (plasmid R721)	0.291134	0.209497	0.21193	0.287439
NC_003295	Ralstonia solanacearum	0.255556	0.246667	0.24	0.257778
NC_000907	Haemophilus influenzae (Rd)	0.353833	0.148793	0.153898	0.343475
NC_002607	Halobacterium sp. (NRC-1)	0.188925	0.313247	0.310605	0.187223
NC_000915	Helicobacter pylori (26695)	0.3593	0.137307	0.154089	0.349304
NC_000921	Helicobacter pylori (J99)	0.351909	0.148488	0.162548	0.337055
NC_002137	Lactococcus cremoris (plasmid pNZ4000)	0.355004	0.145747	0.173055	0.326193
NC_002662	Lactococcus lactis	0.378586	0.124909	0.160222	0.336283
NC_003212	Listeria innocua (Clip11262)	0.351615	0.142858	0.176998	0.328529
NC_003210	Listeria monocytogenes (EGD)	0.346104	0.147406	0.177076	0.329414
NC_002682	Mesorhizobium loti (plasmid pMLb)	0.214231	0.284752	0.291247	0.20977
NC_002678	Mesorhizobium loti	0.218228	0.284727	0.285867	0.211177
NC_000916	Methanobacterium thermoautotrophicum (delta H)	0.319494	0.18352	0.19296	0.304026
NC_000909	Methanococcus jannaschii	0.383845	0.11403	0.129283	0.372843
NC_003551	Methanopyrus kandleri (AV19)	0.200434	0.297155	0.307352	0.195059
NC_003552	Methanosarcina acetivorans (C2A)	0.333612	0.169457	0.174811	0.322119
NC_003901	Methanosarcina mazei (Goe1)	0.335876	0.164747	0.16769	0.331688
NC_002677	Mycobacterium leprae (TN)	0.187086	0.27649	0.321192	0.215232
NC_002755	Mycobacterium tuberculosis (CDC1551)	0.196068	0.302233	0.31504	0.186659
NC_000962	Mycobacterium tuberculosis (H37Rv)	0.196432	0.304403	0.313149	0.186016
NC_000908	Mycoplasma genitalium	0.367269	0.141328	0.14336	0.348044
NC_000912	Mycoplasma pneumoniae	0.336135	0.168198	0.168528	0.327139
NC_002771	Mycoplasma pulmonis	0.422614	0.08577	0.093849	0.397767
NC_003116	Neisseria meningitidis (serogroup A strain Z2491)	0.287045	0.224549	0.220981	0.267426
NC_003112	Neisseria meningitidis (serogroup B strain MC58)	0.293869	0.220158	0.215051	0.270922
NC_003272	Nostoc sp. (PCC 7120)	0.328164	0.176426	0.176844	0.318566
NC_002663	Pasteurella multocida	0.332998	0.163356	0.172938	0.330708
NC_002122	Plasmid ColIb-P9	0.263065	0.244201	0.23187	0.260863
NC_002483	Plasmid F	0.293327	0.199083	0.210064	0.297526
NC_002134	Plasmid R100	0.28753	0.217654	0.223334	0.271481
NC_002516	Pseudomonas aeruginosa	0.203574	0.30486	0.293744	0.197822
NC_003350	Pseudomonas putida (plasmid pWW0)	0.221135	0.283861	0.288276	0.206728
NC_003364	Pyrobaculum aerophilum	0.277496	0.220089	0.2264	0.276015
NC_003296	Pyrobaculum aerophilum	0.277496	0.220089	0.2264	0.276015
NC_000868	Pyrococcus abyssi	0.303426	0.190595	0.203458	0.302522
NC_003413	Pyrococcus furiosus (DSM 3638)	0.31836	0.175281	0.188468	0.317891
NC_000961	Pyrococcus horikoshii	0.318463	0.175196	0.189504	0.316837
NC_003103	Rickettsia conorii (Malish 7)	0.369363	0.138443	0.148575	0.343619
NC_000963	Rickettsia prowazekii (Madrid E)	0.385694	0.112105	0.120806	0.381395
NC_002638	Salmonella Choleraesuis (50k virulence plasmid)	0.269815	0.220568	0.224913	0.284704
NC_003384	Salmonella Typhi (plasmid pHCM1)	0.290802	0.202909	0.21092	0.295369
NC_003385	Salmonella Typhi (plasmid pHCM2)	0.301451	0.210195	0.20977	0.278584
NC_003198	Salmonella Typhi	0.289873	0.208486	0.210412	0.291228
NC_002305	Salmonella typhi (plasmid R27)	0.292833	0.200335	0.210706	0.296126
NC_003277	Salmonella typhimurium (LT2 plasmid pSLT)	0.250919	0.24901	0.251732	0.248339
NC_003197	Salmonella typhimurium (LT2)	0.290432	0.20943	0.209792	0.290345
NC_002698	Shigella flexneri (virulence plasmid pWR501)	0.299489	0.206613	0.214861	0.279037
NC_003047	Sinorhizobium meliloti (1021)	0.221659	0.279783	0.284867	0.213692
NC_003037	Sinorhizobium meliloti (plasmid pSymA)	0.22263	0.279295	0.28446	0.213615
NC_003078	Sinorhizobium meliloti (plasmid pSymB)	0.224171	0.279466	0.285155	0.211207
NC_002758	Staphylococcus aureus (Mu50)	0.373193	0.121018	0.151865	0.353924
NC_002745	Staphylococcus aureus (N315)	0.373372	0.1203	0.149601	0.356727
NC_003098	Streptococcus pneumoniae (R6)	0.350542	0.144933	0.177469	0.327057
NC_003028	Streptococcus pneumoniae (R6)	0.350542	0.144933	0.177469	0.327057
NC_003485	Streptococcus pyogenes (MGAS8232)	0.343958	0.15266	0.187757	0.315626
NC_002737	Streptococcus pyogenes	0.341701	0.154167	0.186625	0.317507
NC_003888	Streptomyces coelicolor (A32)	0.158916	0.349382	0.341986	0.149716
NC_003106	Sulfolobus tokodaii	0.359505	0.138665	0.142451	0.359379
NC_000911	Synechocystis sp. (PCC 6803)	0.288694	0.210883	0.206234	0.294189
NC_003869	Thermoanaerobacter tengcongensis (MB4T)	0.348676	0.140259	0.196223	0.314841
NC_002689	Thermoplasma volcanium	0.343795	0.157582	0.160852	0.337771
NC_000853	Thermotoga maritima	0.311903	0.17974	0.213007	0.29535
NC_000919	Treponema pallidum	0.222977	0.236436	0.296936	0.243651
NC_002488	Xylella fastidiosa (9a5c)	0.267285	0.227061	0.226993	0.278661
NC_003131	Yersinia pestis plasmid (pCD1)	0.30731	0.187034	0.196966	0.30869
NC_003134	Yersinia pestis plasmid (pMT1)	0.288638	0.219575	0.215738	0.27605
NC_003143	Yersinia pestis strain (CO92)	0.300678	0.196472	0.199165	0.303685
Bmelitensis	Brucella melitensis (chr I and II)	0.25082	0.24512	0.253735	0.250325
Vcholerae	Vibrio cholerae (chr I and II)	0.296128	0.200417	0.203164	0.300292
NC_004041	Rhizobium etli (symbiotic plasmid p42d)	0.227587	0.272952	0.277418	0.222043
NC_003450	Corynebacterium glutamicum	0.26862	0.230742	0.235683	0.264956
Dradiodurans	Deinococcus radiodurans (R1)	0.191602	0.313635	0.300836	0.193927

Figures 1 compares the 3th order transition probabilities of two different genomes. In panel A the third-order transition matrices of E.coli and S.typhimurium are compared. The relatedness of both species is reflected by the almost identical distribution of the transition probabilities, which is represented by the scattering of the dots around the 1-1 line. In panel B the same plot is made but for two species with different GC content: E.coli K12 (At-rich) and S.coelicolor A32 (GC rich). From these plots it is clear that exchanging background models of E.coli and S.typhimurium will not deteriorate results obtained by the Motif Sampler. Exchanging background models between organisms with strongly different base pair composition will unmistakably result in an increase of false positives.

comparison of transition probabilities

Figure 1.A	Figure 1.B
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The tree in Figure2 shows the relatedness between organisms based on their oligonucleotide frequency of length 4 (3 order transition probabilities). To construct this tree, each genome was characterized by its transition probability vector of order 3. The Euclidean distance was used to calculate a pairwise distance between all 106 probability vectors. Using complete linkage clustering, a tree was constructed (TREECON, (Van de Peer and De Wachter, 1994)). For organisms or entries clustering together in this tree, background models can safely be exchanged (e.g. the base pair composition of E. coli strains and S. strains are almost identical). If, however, two organisms are too far away in the tree, the use of a distinct background model is essential (see also Fig B). This information can be useful for e.g. phylogenetic footprinting. If one searches a motif in the intergenics of orthologs of distinct organisms by using Motif Sampler, it is advisable to check the background distribution of these species.

Figure 2
[View full size image]