Table 1.

De novo assembly statistics using different BLASTx alignment cutoffs

	Column A; Mammal Filter and e-Value ≤1e−4	Column B: ≥80% of a Swiss-Prot Sequence Matched	Column C: ≥40% Swiss-Prot Sequence Covered and ≥70% identity
K3 assembly: 180,731 contigs with BLASTx result
De novo contigs constructed	46,741	8,055	19,812*
Swiss-Prot sequences aligned	16,465	4,875	9,510*
Swiss-Prot Genes	11,895	4,677	8,433*
K10 assembly: 53,511 contigs with BLASTx result
De novo contigs constructed	26,684	6,478	13,251
Swiss-Prot sequences aligned	13,005	4,498	8,220
Swiss-Prot Genes	10,529	4,336	7,576

Contigs generated by the Trinity de novo assembly using minimum kmer coverage settings 3 and 10 were aligned using BLASTx to the Swiss-Prot database. For each assembly the table shows the number of contigs that pass the filter denoted by the column heading, the number of Swiss-Prot sequences aligned by the contigs, and the number of Swiss-Prot genes matched in the assembly. Column A: filter for BLASTx matches to sequences in mammals with an e-value <1e⁻⁴. Columns B and C: further filtering of the contigs selected by the mammal and e-value filter. Column B: filter for contigs that match identically to ≥80% of the full sequence found in Swiss-Prot. Column C: filter for contigs that cover ≥40% of the Swiss-Prot sequence as determined using a Trinity module and with ≥70% identity to the sequence as reported by BLAST. Details of these filters can be found in materials and methods.

^*Final assembly chosen for further analysis.