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McCarter, J.P. et al. Analysis and functional classification of transcripts from the nematode Meloidogyne incognita.
(See Thomassen et al., [21] for details about the annotation and the classification of transcripts).
There is also a link to the g:Profiler tool that provides functional annotation to assess the biological classification of transcripts with specific expression patterns [42].
GR performed functional classification of transcripts and revised the manuscript.
Additionally, we performed a functional classification of transcripts following the Gene Ontology (GO) scheme with Blast2GO package [ 33].
However, the classification of transcripts is only tentative, since the biological function of many genes identified has not yet been established experimentally.
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Three points must be mentioned with respect to the classification of transcript and enhancer clusters.
Ontology and pathway classification of transcript profiles from the two strains identified an enrichment of genes involved in a number of pathways, including the MAPK, tight junction, insulin signalling and Wnt signalling.
Classification of 2,605 transcripts was consistent between CodeWise and CPC, while 333 transcripts were reclassified by CodeWise.
To that end, an initial step of unsupervised clustering was followed by expert classification of selected transcripts and supervised prediction of cluster membership for all transcripts.
Figure 1 Ds1 termini sequences and classification of exonized transcripts.
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