We use this to assess 15 ab initio and model-based tools representing those most widely used (historically and currently) to generate the knowledge in genomic databases. This makes it possible to identify which performs better for specific use-cases. We present an evaluation framework (ORForise) based on a comprehensive set of 12 primary and 60 secondary metrics that facilitate the assessment of the performance of CDS prediction tools. To date, users have lacked a systematic and replicable approach to identify the strengths and weaknesses of any CoDing Sequence (CDS) prediction tool and allow them to choose the right tool for their analysis. This hinders the discovery of new genomic information as it results in predictions being biased towards existing knowledge. The biases in CoDing Sequence (CDS) prediction tools, which have been based on historic genomic annotations from model organisms, impact our understanding of novel genomes and metagenomes. Of course, some organisms have fallen from grace … Indeed, it is not an exaggeration to say that research on animals has taught us nearly all we know about cell biology-be it transcriptional control, RNA quality control or the structure of chromatin. coli suggests that model organisms can become even more valuable for studying cellular processes once their biology is well understoodĪnimal rights activists have seized on this argument, but show little interest in appreciating the huge contribution that model organisms have made to molecular biology. This is the case at least for research into human diseases, which, after all, drives much of the research in molecular biology. However, several high‐profile clinical trials in which the use of model organisms failed to predict the serious side effects of some drugs, coupled with the prospect of using human stem‐cell lines in trials and the growing sophistication of in silico methods, have all cast doubt on the future use of model organisms. These model organisms became the irreplaceable tools of fundamental biological and clinical research, and helped scientists to amass an enormous amount of knowledge. Over time and with more knowledge to hand, biological research expanded to the study of more complex systems, which required the increasing use of higher organisms, including Caenorhabditis elegans, Drosophila, Arabidopsis, zebrafish and rodents. They reduced the complexity of the task in two ways: they focused on a few central molecular mechanisms-replication, transcription, protein synthesis and the control of gene activity-and they chose to use the simplest organisms-bacteria and bacteriophages-in which to study these phenomena. During the 1940s and 1950s, in the early days of molecular biology, biologists tackled the enormous problem of explaining how cells work at the molecular level by applying the tried and tested tools of reductionism.
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March 2023
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