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Additional work is required to identify effective algorithms to render multiple sequence alignment sonification useful to researchers. For protein multiple sequence alignments, there was limited evidence that the sonifications successfully conveyed information. This entailed a focus group session and survey research by questionnaire of individuals engaged in bioinformatics research.įor single protein sequences, the success of our sonifications for conveying features was supported by both the survey and focus group findings. To do this we focussed on subjective assessments of user experience. For two of these algorithms, we investigated their effectiveness at conveying information. We have created five parameter-mapping sonification algorithms that aim to improve knowledge discovery from protein sequences and small protein multiple sequence alignments. The use of sound to represent sequence data-sonification-has great potential as an alternative and complement to visual representation, exploiting features of human psychoacoustic intuitions to convey nuance more effectively. In conclusion, we demonstrate the potential of an in-depth RNA-seq re-analysis for the guidance of future experiments and to expand on current knowledge. Furthermore, Gm.DHDPS-B expression is significantly upregulated in some but not all stress responses including salt stress, flooding, ethylene or infection with Phytophthora sojae and coincides with downregulation of DHDPS A-types. Gm.DHDPS-B is seen almost exclusively expressed in roots and nodules in addition to old cotyledons or senescent leaves while both DHDPS A-types are expressed constitutively in all tissues analyzed with the highest expression in mature seeds. max DHDPS isozymes in different plant tissues and under various stress conditions, 461 RNA-seq experiments were exploited and re-analyzed covering two expression atlases, 13 abiotic and 5 biotic stress studies.
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To further investigate the expression pattern of the G. max genome comprises two A-type DHDPS genes (Gm.DHDPS-A1 Glyma.09G268200, Gm.DHDPS-A2 Glyma.18G221700) and one B-type (Gm.DHDPS-B Glyma.03G022300). Here, we present a phylogenetic analysis of the DHPDS gene family in land plants which establishes the existence of a legume-specific class of DHDPS, termed DHDPS B-type, distinguishable from the DHDPS A-type commonly present in all land plants. DHDPS isoforms with novel regulatory properties in Medicago truncatula were demonstrated earlier and hypothesized to be involved in abi-otic and biotic stress responses. DHDPS is a key enzyme in the aspartate-derived lysine biosynthesis pathway and an evident object of study for biofortification strategies in plants.