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Table 2 Summary of salmonid ESTs and contig assemblies.

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

  Atlantic salmon Rainbow trout Chinook salmon Sockeye salmon Brook trout Lake whitefish Grayling Northern pike Rainbow Smelt
# EST sequencesa 436629 246704 14535 12056 10051 10842 10975 3624 36785
Assembly Stage1b          
   # contigs (2+)c 70,845 42423 2890 2480 4178 4464 4616 1074 9044
   # singletonsd 47,139 26935 6295 4118 1247 2510 1314 1346 7019
   # transcriptse 117,984 69358 9185 6598 5425 6974 5930 2420 16063
Assembly Stage2f          
   # transcriptsg 81398 51199 8517 6200 4946 6446 5408 2380 12159
   # hitsh 29844 19266 3684 3561 1838 2314 1780 198 6139
   % with hitsi 37 38 43 57 37 36 33 8 50
  1. a number of EST sequences for all of the species including those in GenBank
  2. b Assembly stage 1 refers to PHRAP assembly using parameters 0.99 repeat_frequency and 100 minscore
  3. c number of contigs with 2 or more sequences
  4. d number of contigs with 1 sequence
  5. e total number of transcripts including singletons
  6. f Assembly stage 2 refers to PHRAP assembly using parameters 0.96 repeat_frequency and 300 minscore
  7. 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
  8. h number of transcripts that have a BLASTX hit of < 1e-10 to SwissProt/CDD databases.
  9. i percent of stage 2 assembled transcripts that have a BLASTX hit.