MapMi: automated mapping of microRNA loci

BMC Bioinformatics

Table 1 MapMi mapping results.

Species	Loci in miRBase	Overlapping Loci (1)	New Loci (1)	Overlapping Loci (2)	New Loci (2)
Anopheles gambiae	67	59	27	59	12
Bos taurus	626	517	1002	515	187
Caenorhabditis elegans	174	150	96	150	3
Canis familiaris	325	310	251	309	89
Ciona intestinalis	25	21	5	21	1
Ciona savignyi	27	23	4	23	3
Drosophila melanogaster	157	129	4	129	2
Drosophila pseudoobscura	73	59	33	59	24
Drosophila simulans	70	55	50	55	47
Equus caballus	347	311	332	310	99
Gallus gallus	476	410	172	410	71
Homo sapiens	750	620	874	619	138
Macaca mulatta	483	442	730	440	166
Monodelphis domestica	161	146	162	145	58
Mus musculus	600	428	133	427	51
Ornithorhynchus anatinus	348	289	238	289	58
Pan troglodytes	604	514	751	512	149
Rattus norvegicus	320	297	152	297	60
Takifugu rubripes	133	123	124	122	95
Xenopus tropicalis	208	190	58	190	24
Total Loci in miRBase: 5974		Found: 5093 overlapping loci and 5232 new loci		Found: 5081 overlapping loci and 1365 new loci
Correctly named:		5046		5035
Overlap ratio:		(5093/5974): 85.25%		(5081/5974): 85.05%
Correct Name Ratio:		(5046/5093): 99.07%		(5035/5081): 99.09%

Summary of the number of loci per species that overlap miRBase annotated loci, and the number of times the overlapping loci is correctly named by MapMi. This analysis could not be performed for all species, as miRBase loci coordinates were not readily available. We present results for two different parameter sets. (1) MapMi default parameters with no repeat element post-filtering. (2) MapMi allowing only perfect matches, post-filtering for sequences that are associated with repeat elements and map to multiple places in the genome (details of filtered sequences in Additional file 1, Table S3).

ISSN: 1471-2105