ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation

BMC Genomics

Table 1 Comparison of our repeats searching algorithm with early published ones

Genome	Repeat type	Our algorithm ¹	Vmatch imperfect ²	Vmatchperfect ³	RepEx ⁴	Repeat-Around ⁵
*Homo sapiens*	direct	6304 (6135 impf. 169 pf.)	2507 (2507 impf.) 1358 common	320 pf., common	–	333 pf., t.l.
	complimentary	1694 (1654 impf. 40 pf.)	–	–	70 pf., common	7 pf., t.l.
	mirror	5416 (5295 impf. 121 pf.)	–	–	252 pf., common	83 pf., t.l.
	inverted	1939 (1868 impf. 71 pf.)	1984 (1974 impf., 10 pf.) 1937 common	127 pf., common	110 pf., common	35 pf., t.l.
*Mus musculus*	direct	6765 (6594 impf. 171 pf.)	2543 (2543 impf.) 1325 common	308 pf., common	–	323 pf., t.l.
	complimentary	3580 (3511 impf. 69 pf.)	–	–	143 pf., common	50 pf., t.l.
	mirror	6029 (5871 impf. 158 pf.)	–	–	286 pf., common	97 pf., t.l.
	inverted	3873 (3772 impf. 101 pf.)	3947 (3929 impf. 18 pf.) 3853 common	195 pf., common	179 pf., common	63 pf., t.l.

¹impf. and pf. denotes imperfect and perfect repeats, respectively
²Vmatch run options for imperfect repeats finding: 1) for direct repeat length 10 the allowed hamming distance 1 (90% identity), for direct repeat lengths from 11 to 100 the allowed hamming distance is integer of L/5, where L is the repeats length (80% identity) ‘– supermax’ option was used for all repeat lengths, 2) for inverted repeat lengths with lengths from 10 to 100 the allowed hamming distance is varied from 1 to 10 for each length (minimum identity seeks from 90 to 80% with repeat length growth). After the repeats retrieval, all doubles were disregarded as well as inner repeats (or sub-repeats) with a smaller length than searched; all intersected repeats were merged into longer ones. “Common” denotes common repeat patterns between our algorithm and previous three algorithm
³Vmatch run options for perfect repeats finding: ‘-identity 100’ option, repeat lengths from 10 to 100 for direct and inverted repeats
⁴RepEx run options: minimum length 10; spacer intervals greater than 0; sequence degeneracy allowed
⁵RepeatAround run options: repeat lengths from 10 to 256. RepeatAround “t.l.” denotes typical locations or, in other words, locations matched graphically by hand with repeat positions found by our algorithm (see details in text)

ISSN: 1471-2164