FONZIE: An optimized pipeline for minisatellite marker discovery and primer design from large sequence data sets

BMC Research Notes

Table 1 FONZIE results when performed on different fungal or oomycetes whole genomes.

				Nb of markers identified^c			Nb of amplification products (AP) and primers designed^d
Organism	Genome Size (Mb)	Nb of contigs or super contigs^a	Execution Time^b	Total	Single copy	Multiple copies	Single copy	Multiple copies	No primers	No BLAST results	% single-copy AP
Aspergillus niger	34.85	24	2 min 53 sec	637	533	104	600	18	17	2	94.19
Stagonospora nodorum	37.21	108	4 min 41 sec	1288	978	310	959	154	169	6	74.46
Pyrenophora tritici repentis	37.84	47	5 min 12 sec	1141	878	263	935	195	8	3	81.94
Botrytis cinerea	42.66	588	12 min 03 sec	3648	2719	929	3339	118	176	15	91.53
Leptosphaeria maculans	45.12	76	23 min 36 sec	2606	1799	807	2405	146	49	6	92.29
Laccaria bicolor	64.88	665	45 min 39 sec	5393	1516	3877	1640	3409	338	6	30.41
Phytophthora infestans	228.54	4921	3 h 21 min 37 sec	7514	1855	5659	1718	5239	553	4	22.86

^a Number of sequences in the Multifasta file
^b Machine used for this test: Laptop Intel Core 2 Duo, 2.4 GHz and 3Go RAM
^c FONZIE results after step d of the workflow (Figure 1), using the TRF default parameters (match = 2, indel = 7, mismatch = 7, pi = 10, pm = 80, minscore = 50, maxperiod = 500) and screen parameters for core motif size >3, % identity between motifs = 90%, BLAST cut-off value = 1e-10)
^d Final FONZIE results after steps e (Primer pair design) and f (checking for the specificity of the amplification product) of the workflow shown in Figure 1, using a BLAST cut-off value of 1e-40

ISSN: 1756-0500