A salmonid EST genomic study: genes, duplications, phylogeny and microarrays

BMC Genomics

Table 3 Cross-species comparisons of contig transcripts.

	# contigs	# missing in AS^a	# missing in RT^b	# missing in both^c	% sim to AS^d	Avelen^e	% sim to RT^f	Avelen
Atlantic salmon (SJ)^g	5781	479	1210	354	98.4	705	93.4	493
Atlantic salmon (all)^h	81398	na	36351	na	na	na	93.3	504
Rainbow trout	50256	13626	na	na	93.8	495	na	na
Chinook salmon	8517	797	1224	426	94.2	510	95.5	510
Sockeye salmon	6200	577	770	298	94.6	571	95.7	569
Brook trout	5424	285	627	174	94.4	580	93.9	522
Lake whitefish	6446	804	1420	608	92.5	425	92.2	399
Grayling	5408	657	1136	506	91.7	435	91.3	400
Northern pike	2380	1894	2001	1846	89.6	241	89.4	251
Rainbow smelt	12159	7462	7812	6920	86.2	431	86.1	419

^a number of contigs that are not found in the Atlantic salmon database
^b number of contigs that are not found in the rainbow trout database
^c number of contigs that are not found in either the Atlantic salmon or rainbow trout database
^d percent identity compared to the top BLASTN hit to the Atlantic salmon database over 200 bp and e-value < 1e-25. In the case of Atlantic salmon (SJ) the comparison is to the McConnell strain.
^e average length of the BLASTN hit
^f percent identity compared to the top BLASTN hit to the rainbow trout database over 200 bp and e-value < 1e-25
^g only Atlantic salmon ESTs from the Saint John River strain
^h all Atlantic salmon ESTs other than those in note "g" above

ISSN: 1471-2164