As summarized in Table 1, a total of 9979 clones were sequenced from the M. tardigradum library generated from two stages, active and inactive, in order to obtain various transcripts and to extract putative anhydrobiotic candidate genes.
We produced 18 libraries (Table 1) from 15 different tissues or stages of the brown planthopper (BPH) to obtain various transcripts and to extract tissue-specifically expressed genes or planthopper-specific genes from the libraries.
These studies indicate that it is beneficial to use expressed transcript information to extract potential miRNA sequences.
The Cufflinks' output annotation file was then compared with adapted annotation to filter out all transcripts overlapping known transcripts or, in other words, to extract intergenic transcripts.
The complexity of the regulatory network (i.e., many miRNAs affecting many target transcripts) makes it difficult to extract individual miRNA/target transcript interactions likely obscuring specific inverse correlations between the expression changes of miRNAs and their targets.
Two of these, Oases [ 2, 3] and trans-ABySS [ 5, 6] start with constructing de Bruijn graphs directly from sequencing reads, remove potential errors, and then resolve each de Bruijn graph to extract transcripts for each connected component (i.e. cluster, or "locus") in the graph.
To avoid redundant transcripts, in-house Perl scripts were applied to extract the longest transcripts as unigenes.
However, to extract transcript populations for candidates with pronounced stress responses is a crucial task.
In each of the assemblies, the reads are used to build a de Bruijn graph, which is then simplified for errors, organized into a scaffold, divided into loci and finally analyzed to extract transcript assemblies or transfrags.
