Detecting microsatellites within genomes: significant variation among algorithms

Leclercq, Sébastien; Rivals, Eric; Jarne, Philippe

doi:10.1186/1471-2105-8-125

BMC Bioinformatics

Table 5 RepeatMasker, STAR, Mreps, TRF and Sputnik detections between starting positions 532800 and 53500 in the human X chromosome.

From: Detecting microsatellites within genomes: significant variation among algorithms

	start	end	divergence	motif	sequence
RepeatMasker
	531688	531713	0	AAT	AATAATAATAATAATAATAATAATAA
	532355	532540	15.05	TTCC	TTCCTTCCTCCCTTCCTTCCTTCCTTTCTTCTTTCTTTCTTTCCTTCCTTCCTGCTTTCCTTCCTTCC
					TTTCTTTTCTTTCTTTCCTTCCTTCCTTGCTTCCTTCCTTCCATCTTTCTCTTTCTCTTTTTCTTTCT
					TTCTCTCCTTCCTTCTTTCCTTCCTTCCTTCCCTTCCCTTCCTTCCTTCC
	532704	532891	15.87	TTCC	CCTTCCTTCCTTTCTTCTTTCTTTCCTTCCTTCCTTGCTTCCTTCCTTCCATCTTTCTTTCTTTCTTT
					CTTCCTCTCCTTCCTTCTTTCCTTCCTTCCTTCCCTTCCCTCCTTCCTTTTTCTTCTTCTCTTTCTTT
					CTTTCTCTTTCCTTCCTTCCTTCCTTCTTTCTCCTTCCTTCCTTCTTTCCTT
STAR
	531688	531713	0	AAT	AATAATAATAATAATAATAATAATAA
	532537	532731	25.38	TTTTTC	TTCCTTTTTCTTCTTCTCTTTCTTTCTTTCTTTTTCTTTCCTTCCTTCCTTCTTTCTCCTTCCTTCCT
					TCCATTTTTCTTTCTTTCTTTCTTTCTTTCTCTCTCTCTCTTTCTTTCTTTCTCTCTCTCTCTTCTTC
					CTTCCTTCCTTCCATTCTTCTTTCTTTCTTTCCTTCCTTCCTTTCTTCTTTCTTTCCTT
Mreps
	531688	531715	3.45	AAT	AATAATAATAATAATAATAATAATAAAA
	532330	532429	15.84	TTCC	TTTCCTTCTTTCTTTCTTACTTTCTTTCCTTCCTCCCTTCCTTCCTTCCTTTCTTCTTTCTTTCTTTC
					CTTCCTTCCTGCTTTCCTTCCTTCCTTTCTTT
	532428	532467	12.5	TTCC	TTTCTTTCTTTCCTTCCTTCCTTGCTTCCTTCCTTCCATC
	532466	532490	4	TTTCTC	TCTTTCTCTTTCTCTTTTTCTTTCT
	532491	532524	11.76	TTCC	TTCTCTCCTTCCTTCTTTCCTTCCTTCCTTCCCT
	532525	532542	5.56	TTCC	TCCCTTCCTTCCTTCCTT
	532551	532593	13.95	TTTC	TCTCTTTCTTTCTTTCTTTTTCTTTCCTTCCTTCCTTCTTTCT
	532593	532609	5.88	TTCC	TCCTTCCTTCCTTCCAT
	532609	532667	16.95	TC	TTTTTCTTTCTTTCTTTCTTTCTTTCTCTCTCTCTCTTTCTTTCTTTCTCTCTCTCTCT
	532667	532689	8.7	TTCC	TTCTTCCTTCCTTCCTTCCATTC
	532690	532756	11.94	TTCC	TTCTTTCTTTCTTTCCTTCCTTCCTTTCTTCTTTCTTTCCTTCCTTCCTTGCTTCCTTCCTTCCATC
	532755	532777	4.35	TTTC	TCTTTCTTTCTTTCTTTCTTCCT
	532776	532820	8.89	TTCC	CTCTCCTTCCTTCTTTCCTTCCTTCCTTCCCTTCCCTCCTTCCTT
TRF {2,7,7;20}
	531688	531713	0	AAT	AATAATAATAATAATAATAATAATAA
	532313	532330	5.26	TTTTC	TTTTCTTTTCTTTCTTTT
	532423	532438	5.88	TTTTC	TTTCTTTTCTTTCTTT
	532466	532490	4	TTTCTC	TCTTTCTCTTTCTCTTTTTCTTTCT
	532544	532553	0	TTC	TTCTTCTTCT
	532550	532576	13.79	TTTCTC	TTCTCTTTCTTTCTTTCTTTTTCTTTC
	532633	532667	8.57	TC	TCTCTCTCTCTCTTTCTTTCTTTCTCTCTCTCTCT
Sputnik {1,-6,7}
	531568	531576	0	ACC	ACCACCACC
	531688	531711	0	AAT	AATAATAATAATAATAATAATAAT
	531849	531856	0	TTGC	CTTGCTTG
	531893	531900	0	TG	TGTGTGTG
	531927	531934	0	ATGC	TGCATGCA
	532078	532085	0	AGGC	GCAGGCAG
	532266	532273	0	ATGC	TGCATGCA
	532313	532322	0	TTTTC	TTTTCTTTTC
	532335	532354	5	TTTC	TTCTTTCTTTCTTACTTTCT
	532355	532422	10.29	TTCC	TTCCTTCCTCCCTTCCTTCCTTCCTTTCTTCTTTCTTTCTTTCCTTCCTTCCTGCTTTCCTTCCTTCC
	532423	532439	5.88	TTTC	TTTCTTTTCTTTCTTTC
	532440	532463	4.17	TTCC	CTTCCTTCCTTGCTTCCTTCCTTC
	532466	532489	4.17	TTTCTC	TCTTTCTCTTTCTCTTTTTCTTTC
	532500	532541	7.14	TTCC	TCCTTCTTTCCTTCCTTCCTTCCCTTCCCTTCCTTCCTTCCT
	532544	532552	0	TTC	TTCTTCTTC
	532553	532568	0	TTTC	TCTTTCTTTCTTTCTT
	532569	532576	0	TTTC	TTTCTTTC
	532577	532588	0	TTCC	CTTCCTTCCTTC
	532596	532607	0	TTCC	TTCCTTCCTTCC
	532615	532656	7.14	TTTC	TTTCTTTCTTTCTTTCTTTCTCTCTCTCTCTTTCTTTCTTTC
	532657	532666	0	TC	TCTCTCTCTC
	532669	532684	0	TTCC	CTTCCTTCCTTCCTTC
	532687	532692	0	TTC	TTCTTC
	532693	532704	0	TTTC	TTTCTTTCTTTC
	532705	532752	8.33	TTCC	CTTCCTTCCTTTCTTCTTTCTTTCCTTCCTTCCTTGCTTCCTTCCTTC
	532755	532774	0	TTTC	TCTTTCTTTCTTTCTTTCTT
	532780	532820	7.32	TTCC	CCTTCCTTCTTTCCTTCCTTCCTTCCCTTCCCTCCTTCCTT

Resolution of Mreps was set to 1, threshold alignment score of TRF to 20 and alignment weights of TRF to {2,7,7}. Sputnik mismatch penalty and validation score were set to -6 and 7, respectively. The number of detections varies with algorithms (from 3 to 18). Moreover, the sequence information is dealt with in different ways; an example is the region of cryptic simplicity between positions 532815 and 533080. RepeatMasker and STAR decompose it into large, distant and highly imperfect detections, though not the same for the two algorithms. Mreps returns a succession of shorter detections, overlapping the whole region. TRF detects only short, not much divergent, subregions, which do not completely overlap with the whole region. Sputnik detections are very numerous, short and slightly divergent, but overlap the whole region. Detection of compound microsatellites by Mreps is illustrated at position 533706, where other algorithms detect only a perfect polyA strech. The detection at position 534186 is returned as two detections by Mreps, because the two consecutive errors (insertions of G and C) stop the detection when resolution is set to 1. Very short hexanucleotides (12 bp) are detected by both TRF and Sputnik at positions 533138 and 534112. Most detections of Sputnik are two-repeat tetranucleotides, or three-repeat trinucleotides, which cannot be detected by other algorithms.

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ISSN: 1471-2105

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