Table 3.

Summary of the de novo annotation step for the four assembled transcriptomes.

	S. pombe	C. sinensis	O. sativa	D. melanogaster
# transcripts	9,370	201,892	166,512	80,999
# Blast Hits	8,257	72,559	66,129	29,924
# Annotations	3,922	51,272	50,721	22,534
% of annotated transcripts	42%	25%	30%	28%
# HMMER hits	5,588	34,689	28,736	16,552
User time	11 h	3 d 19 h	6 d 8 h	4 d 15 h

Notes: # Transcripts, number of transcripts assembled by Trinity; # Blast hits, number of transcripts with at least one hit against the NCBI nr database (e-value <10⁻⁶); # Annotation, number of transcripts with at least one annotation after Blast2GO analysis; # HMMER hits, number of transcripts with at least one hit against the Pfam A database (e-value <10⁻⁶); User time, time needed to perform the complete pipeline (cleaning, assembly, annotation, and expression quantification).