M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species

Table 1 A summary of experimental results for 23 distinct sets of sequences

#	Sequence set	Size	$A$ _size	$A$	$ℳ$	$C$	t _anchor	t _mum	t _total	Mem	Cov.
1	Mycoplasma 2	1.5	22	264	6325	649	2s	5s	8s	52	72.8
2	Pyrococcus 2	3.5	23	1159	3229	484	6s	3s	9s	153	62.5
3	Salmonella 2	9.6	27	470	516	39	16s	1s	17s	419	98.9
4	Listeria 3	8.7	24	13101	45940	722	16s	114s	143s	283	94.3
5	X. Campestris 3	15.3	27	15843	37702	2441	25s	151s	181s	487	74.8
6	P. Syringae 3	18.4	27	11232	39753	1527	35s	252s	294s	573	72.8
7	C. Pneumoniae 4	4.9	21	770	0	7	6s	0s	6s	156	98.5
8	Yersinia 4	21.4	25	14049	6	400	24s	1s	25s	488	94.0
9	Shigella 5	23.1	23	37596	1285	564	32s	2s	38s	548	76.7
10	Salmonella 5	23.8	23	46336	983	328	35s	1s	39s	567	93.1
11	E. Coli 5	25.3	23	47221	5543	704	38s	9s	57s	553	84.2
12	Streptococcus 7	13.1	21	15446	84	121	17s	1s	18s	258	88.3
13	Staphylococcus 7	19.6	24	23216	132	260	24s	2s	26s	390	92.6
14	Bacillus 7	36.8	25	27731	4149	468	54s	7s	62s	713	93.2
15	Entero 10 (9&11)	48.4	23	39979	3753	418	63s	12s	78s	740	73.3
16	Entero 15 (9&10&11)	72.2	23	5802	8136	1218	95s	84s	181s	991	54.9
17	Entero 19 (8&9&10&11)	93.6	18	1132	637	907	161s	99s	261s	1174	15.6
18	Bacilli 14 (12&13)	22.7	19	251	3801	2721	43s	41s	93s	414	14.3
19	Bacilli 14 (13&14)	56.4	19	431	5250	2718	79s	100s	185s	654	26.3
20	Bacilli 21 (12&13&14)	62.3	15	597	1691	2045	100s	54s	155s	638	4.1

A selection of results for 20 independent sets of closely related sequence comparisons conducted with M-GCAT. Size and Memory usage are listed in megabytes (MB). All experiments were performed and running times (cpu time) measured on a 2 GHZ Pentium processor, with 2 GB of main memory, running Windows XP Professional. Size is the total size (MB) of the set of sequences. $A$ is the number of multi-MUM Anchors found, $A$ _sizeis the configured minimum size of multi-MUM Anchors, $ℳ$ is number of multi-MUMs found, $C$ is the number of multi-MUM clusters. t_anchoris the time needed to find the set of multi-MUM anchors, t_mumis the time needed to find the initial set of multi-MUMS, and t_totalthe time required to perform entire comparison. Mem is peak usage of system memory (MB), and Cov. is the percentage of each sequence that was aligned. The percentage that was not aligned corresponds to regions where no multi-MUMs were found. A p value of 10,000,000 and q value of 100 was used for all experiments. The d value was set to the length of the longest sequence in each example to emphasize the global alignment framework. For a complete listing of the sequences used in these comparisons refer to Additional file 2.

ISSN: 1471-2105