Markup | Genome Research

Table 1.

Assignment Statistics for Each Genome

Organism	Celeg	sacc	aero	aful	mjan	mthe	pabyssi
Total residues	7687386	2973530	638684	662214	480086	526546	535767
Total coverage	780323	379345	110547	162470	104799	116705	126282
Percentage covered	10.15	12.76	17.31	24.53	21.83	22.16	23.57
Remaining residues	6907063	2594185	528137	499744	375287	409841	409485
Potential extra domains	69070.6	25941.9	5281.37	4997.44	3752.87	4098.41	4094.85
Genes	16315	6284	2694	2388	1704	1855	1764
Domains assigned	7438	3259	871	1388	875	986	1022
No. of genes with assignment	3960	1897	512	799	538	610	617
Percent of genes assigned	24.27	30.19	19.01	33.46	31.57	32.88	34.98
Organism	Pyro	aquae	bbur	bsub	Cjej	cpneu	cpneuA
Total residues	568465	482512	282455	1216011	508329	361654	362202
Total coverage	118997	124311	61327	313853	120715	72247	72085
Percentage covered	20.93	25.76	21.71	25.81	23.75	19.98	19.90
Remaining residues	449468	358201	221128	902158	387614	289407	290117
Potential extra domains	4494.68	3582.01	2211.28	9021.58	3876.14	2894.07	2901.17
Genes	2062	1522	825	4072	1619	1051	1067
Domains assigned	961	1052	514	2660	993	597	595
No. of genes with assignment	574	606	290	1493	588	335	333
Percent of genes assigned	27.84	39.82	35.15	36.67	36.32	31.87	31.21
Organism	Ctra	dra1	ecoli	hinf	hpyl	hpyl99	mgen
Total residues	312177	777034	1358281	520535	495345	493679	174922
Total coverage	68776	181767	341229	147433	101455	101180	42767
Percentage covered	22.03	23.39	25.12	28.32	20.48	20.50	24.45
Remaining residues	243401	595267	1017052	373102	393890	392499	132155
Potential extra domains	2434.01	5952.67	10170.5	3731.02	3938.9	3924.99	1321.55
Genes	894	2577	4266	1694	1523	1482	479
Domains assigned	581	1518	2677	1200	803	801	353
No. of genes with assignment	322	890	1597	683	473	475	196
Percent of genes assigned	36.02	34.54	37.44	40.32	31.06	32.05	40.92
Organism	Mpneu	mtub	nmenA	paer	rpxx	Synecho	tmar
Total residues	237564	1329160	584613	1859257	278955	1032549	580647
Total coverage	45848	307541	138067	458736	70406	222185	144015
Percentage covered	19.30	23.14	23.62	24.67	25.24	21.52	24.80
Remaining residues	191716	1021619	446546	1400521	208549	810364	436632
Potential extra domains	1917.16	10216.2	4465.46	14005.2	2085.49	8103.64	4366.32
Genes	674	3915	2026	5557	831	3151	1813
Domains assigned	369	2579	1144	3910	580	1893	1181
No. of genes with assignment	208	1440	673	2212	326	1112	675
Percent of genes assigned	30.86	36.78	33.22	39.81	39.23	35.29	37.23
Organism	Tpal	uure	vcho1	xfas
Total residues	349767	227646	855150	738838
Total coverage	69848	38947	208440	164002
Percentage covered	19.97	17.11	24.37	22.20
Remaining residues	279919	188699	646710	574836
Potential extra domains	2799.19	1886.99	6467.1	5748.36
Genes	1007	609	2593	2669
Domains assigned	598	330	1756	1320
No. of genes with assignment	334	194	969	784
Percent of genes assigned	33.17	31.86	37.37	29.37

[i] The first of the rows gives the total number of residues within an organism's genes available for structural assignment. The next rows give the number of residues that have a structural assignment and percentage of residues that have an assignment. To complement this the amount of residues left to annotate can provide a crude estimate of how many extra structural domains may be present. This was simply calculated by dividing the remaining residues by a typical domain length of 100 residues (Pearl et al. 2001). The next rows quote the number of genes in the organism, the number of structural domains that have been assigned, and the number of genes that have one or more structural assignments. Finally all of this is summarized as a percentage of genes that have one or more structural assignments.

[ii] celeg: Caenorhabditis elegans; sacc: Saccharomyces cerevisiae; aero: Aeropyrum pernix; aful:Archeoglobus fulgidus; mjan: Methanococcus jannaschii; mthe: Methanobacterium thermoautotrophicum;pabyssi: Pyrococcus abyssi; pyro: Pyrococcus horikoshii; aquae: Aquifex aeolicus; bbur: borrelia burgdoferi; bsub: bacillus subtillus; cjej:Campylobacter jejuni; cpneu: Chlamydia pneumonia;cpneuA: Chlamydophilia pneumoniae; ctra: Chlamydia trachomatis; dra1: Deinococcus radiodurrans; ecoli:Escherichia coli; hinf: Haemophilus influenzae; hpyl:Helicobacter pylori; hpyl99: Helicobacter pylori J99;mgen: Mycoplasma genitalium; mpneu: Mycoplasma pneumoniae; mtub: Mycobacterium tuberculosis; nmenA:Neisseria meningitidis; paer: Pseudomonas aeruginosa;rpxx: Rickettssia prowazekii; syencho: Synechocystis PCC86803; tmar: Thermotoga maritima; tpal: Treponema pallidum; uure: Ureaplasma urealyticum; vchol: Vibrio cholerae; xfas: Xylella fastidiosa.