web-based browser interface  (Epilogos Charities)

Journal: Plant Molecular Biology

Article Title: Elucidating and mining the Tulipa and Lilium transcriptomes

doi: 10.1007/s11103-016-0508-1

Figure Lengend Snippet: Effect of transcriptome filtering on the percentage of “non-plant” and plant transcripts retained. Filtering done based on counts per transcript and transcripts per million

Article Snippet: Subsequently, a web-based interface (Kamei et al. ), which we call Transcriptome Browser, was implemented for data presentation and mining.

Techniques:

Journal: Plant Molecular Biology

Article Title: Elucidating and mining the Tulipa and Lilium transcriptomes

doi: 10.1007/s11103-016-0508-1

Figure Lengend Snippet: Screenshots of the Transcriptome browser. In panel 1 the interphase of the BLAST search is shown. The input sequence can be blasted against the tulip and lily transcriptomes as well as other plants species such as Arabidopsis thaliana, Oryza sativa and Vitis vinifera . In panel 2 an example is given of the output of the cluster search. Here different actions can be chosen such as protein alignment, primer design and build a direct tree (phylogenetic tree). Note that the browser has a tutorial option, in which the exact procedure how to perform the different tasks and actions is explained

Article Snippet: Subsequently, a web-based interface (Kamei et al. ), which we call Transcriptome Browser, was implemented for data presentation and mining.

Techniques: Sequencing