ISOL@: an Italian SOLAnaceae genomics resource

BMC Bioinformatics

Table 1 Statistics on the EST collections.

family	genus	sub-genus	species	total EST	nr ESTs	gene indices	TC	sEST	total transcripts	ESTs mapped	TCs mapped
Solanaceae	Solanum	Lycopersicum	SOLLC	250552	190763	44759	17629	28005	45634	14286	975
Solanaceae	Solanum	Lycopersicum	SOLPN	8346	6888	3863	730	3140	3870	488	37
Solanaceae	Solanum	Lycopersicum	SOLHA	8000	7868	4101	907	3203	4110	306	30
Solanaceae	Solanum	Lycopersicum	SOLLP	1008	979	744	94	650	744	3	0
Solanaceae	Solanum		SOLTU	226805	206696	62752	19732	44138	63870	5785	584
Solanaceae	Solanum		SOLCH	7752	7750	7192	306	6886	7192	139	10
Solanaceae	Nicotiana		TOBAC	74940	67745	37845	7529	30578	38107	403	74
Solanaceae	Nicotiana		NICBE	27010	24784	9420	3206	6315	9521	95	21
Solanaceae	Nicotiana		NICLS	12448	11749	6785	958	5840	6798	40	6
Solanaceae	Nicotiana		NICSY	8580	8425	7534	512	7023	7535	68	4
Solanaceae	Nicotiana		NICAT	329	324	312	11	301	312	3	0
Solanaceae	Capsicum		CAPAN	31089	28664	15703	3474	12262	15736	373	67
Solanaceae	Capsicum		CAPCH	372	372	343	11	332	343	4	0
Solanaceae	Petunia		PETHY	10670	10336	7004	1166	5842	7008	31	4
Rubiaceae	Coffea		COFCA	46907	38308	16121	4494	11713	16207	20	10
Rubiaceae	Coffea		COFAR	1071	1059	1007	42	965	1007	3	1

species: SOLLC: Solanum lycopersicum; SOLPN: Solanum pennellii; SOLHA: Solanum habrochaites; SOLLP: S. lycopersicum X S. pimpinellifolium; SOLTU: Solanum tuberosum; SOLCH: Solanum chacoense; TOBAC: Nicotiana tabacum; NICBE: Nicotiana benthamiana; NICLS: Nicotiana langsdorffii x Nicotiana sanderae; NICSY: Nicotiana sylvestris; NICAT: Nicotiana attenuata; PETHY: Petunia x hybrida; CAPAN: Capsicum annuum; CAPCH: Capsicum chinense; COFCA: Coffea canephora; COFAR: Coffea arabica.
nr EST: non-redundant ESTs. It is the number of EST sequences obtained after the removal of over-represented ESTs from each collection. Gene indices are created by grouping overlapping EST sequences into clusters. Each cluster corresponds to a unique gene. TCs: tentative consensus; TCs are generated from multiple sequence alignments of ESTs (assembling process). sESTs: singleton ESTs. The total transcripts number is obtained adding the TCs to the sESTs. The number of ESTs and TCs which are mapped onto the S. lycopersicum genome is included too.

ISSN: 1471-2105