Table 1

Summary of piRNA cluster identification methods and results from previous studies

study

organism

identified clusters

criteria for detection of clusters


Aravin et al. 2006 [3]

human/mouse

14/42

at least 4 piRNA loci per cluster, maximum distance between two piRNA loci 15 kb


Girard et al. 2006 [4]

human/mouse/rat

186/123/157

at least 5 piRNA loci/5kb, at least 10 piRNA loci per cluster, only sequence reads that mapped 1-5 times to the genome were considered, sequence reads mapped to genome allowing up to 2 mismatches


Lau et al. 2006 [5]

mouse/rat

94/100

at least 20 single-copy loci, at least 1 piRNA locus/kb


Lakshmi and Agrawal 2007 [7]

human/mouse/rat

114/2710/189

at least n** single-copy loci/20kb, at least 2 piRNA loci/kb


Grivna et al. 2006 [12]

mouse

35

*


Watanabe et al. 2006 [13]

mouse

34

p < = 0.05, where p = (s/S)n-1×NCn S: genome size (bp), s: cluster size (bp), N: total number of sequence hits, n: number of hits in cluster


*method not explained in more detail, ** based on hit density for each organism [7].

Rosenkranz and Zischler BMC Bioinformatics 2012 13:5   doi:10.1186/1471-2105-13-5

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