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

BMC Genomics

Table 2 Summary of salmonid ESTs and contig assemblies.

	Atlantic salmon	Rainbow trout	Chinook salmon	Sockeye salmon	Brook trout	Lake whitefish	Grayling	Northern pike	Rainbow Smelt
# EST sequences^a	436629	246704	14535	12056	10051	10842	10975	3624	36785
Assembly Stage1^b
# contigs (2+)^c	70,845	42423	2890	2480	4178	4464	4616	1074	9044
# singletons^d	47,139	26935	6295	4118	1247	2510	1314	1346	7019
# transcripts^e	117,984	69358	9185	6598	5425	6974	5930	2420	16063
Assembly Stage2^f
# transcripts^g	81398	51199	8517	6200	4946	6446	5408	2380	12159
# hits^h	29844	19266	3684	3561	1838	2314	1780	198	6139
% with hitsⁱ	37	38	43	57	37	36	33	8	50

^a number of EST sequences for all of the species including those in GenBank
^b Assembly stage 1 refers to PHRAP assembly using parameters 0.99 repeat_frequency and 100 minscore
^c number of contigs with 2 or more sequences
^d number of contigs with 1 sequence
^e total number of transcripts including singletons
^f Assembly stage 2 refers to PHRAP assembly using parameters 0.96 repeat_frequency and 300 minscore
^g the number of transcripts that result from a re-assembly of all stage 1 transcripts using PHRAP parameters 96 repeat_frequency and 300 minscore
^h number of transcripts that have a BLASTX hit of < 1e-10 to SwissProt/CDD databases.
ⁱ percent of stage 2 assembled transcripts that have a BLASTX hit.

ISSN: 1471-2164