Apart from the database annotation of the assembled scaffolds these were also queried for intron length, intron distribution and gene density determination using AUGUSTUS v2.5.5 [ 68] with N. tabacum and S. lycopersicum as references.
For each NM id, we also find the TSS annotated by RefSeq, and treat them as additional ATSS if they are more than 5 base pairs apart from the DBTSS annotation.
Apart from the identified annotated proteins from the reference Nipponbare sequence, two significantly up-regulated proteins under water deficit and combined stress had no sequence annotation available with the existing database (Table 3).
Apart from annotation of the transcriptome, another major goal of RNA-Seq studies is to quantify transcript levels [ 14].
Apart from being given the annotation guidelines with a few examples with screen captures of the system, the annotators did not receive any training on how to use the annotation editor.
Apart from mutations annotation, we also show that deletion mutations in YRS and HRS likely disrupt their dimeric assemblies, which in turn would lead to stalling of new protein translation.
Several of the hub TFs (defined as TFs predicted as having >10 targets and listed in Table 5) have biologically relevant annotations: apart from the interferon responsive TFs Irf1 and Irf7, we find Hoxc6 (associated with cytomegalovirus infection) and cancer-associated TFs such as Egr1, Bmyc and Pbx2, reinforcing the deep connections of the immune response with cancer (de Visser et al., 2006).
We understand that to encourage and sustain high-quality annotation activity, apart from the peer review system and organizational hierarchy, there should be enough incentives to sustain the endeavor.
Apart from ESTIMA, functional annotation of the S. gregaria EST sequences was also performed by means of the software package 'Blast2GO' [35], [35].
Apart from metabolism-related annotations, the KAAS server also provides annotations related to genetic and environmental information processing and cellular processes.
