Table 1.

Salmonid EST Project Summary Statistics^a

	Atlantic salmon^b	Rainbow trout^c	Chinook salmon^d	Sockeye salmon^e	Lake whitefish^f
Number of good sequences^g	61,819^h	14,544	1317	1243	1465
Average trimmed EST length (bp)ⁱ	563	484	492	456	486
Number of contigs^j	11,560	2370	136	291	138
Number of singletons	17,150	6611	949	229	1038
Number of putative transcripts	28,710	8981	1085	520	1176
Max. assembled sequence size (no. of ESTs)	252	93	10	21	28
Average assembled sequence size (no. of ESTs)	2.15	1.61	1.21	2.39	1.24
Number of assembled ESTs with^k
Significant BLASTX hits	10,511	3562	239	337	253
Significant BLASTN hits	13,459	4337	462	331	466
No significant BLAST hits	11,802	3667	566	118	663
Percentage with no significant BLAST hits^k	41.1	40.8	52.2	22.7	56.4
Number of contigs containingⁱ
2 ESTs	5606	1360	90	108	97
3 ESTs	2322	454	26	96	21
4-5 ESTs	2030	350	12	48	9
6-10 ESTs	1149	145	8	32	8
11-20 ESTs	331	41	0	6	1
21-30 ESTs	67	12	0	1	2
31-50 ESTs	36	4	0	0	0
>50 ESTs	19	4	0	0	0

↵a Assembled from the March 3, 2003, version of the GRASP EST database using PHRAP. Results of CAP3 and stackPACK assemblies of the March 3, 2003 GRASP EST database are available at http://web.uvic.ca/cbr/grasp
↵b Salmo salar
↵c Oncorhynchus mykiss
↵d Oncorhynchus tshawytscha
↵e Oncorhynchus nerka
↵f Coregonus clupeaformis
↵g A sequence is considered “good” if its trimmed PHRED20 length is at least 100 bases.
↵h Includes 55.082 good forward (3′) and 6737 good reverse (5′) reads. Of 5606 good reverse reads from clones with good forward reads, 2268 overlap/cluster with the corresponding forward reads.
↵i Vector, low-quality, and contaminating bacterial sequences are trimmed.
↵j A contig (contiguous sequence) contains two or more ESTs.
↵k Threshold for BLASTN and BLASTX significance: 10^-5

Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics