![]() For example, given that BLAST has been designed to retrieve homologs, there are several steps in the BLAST program that incorporate molecular evolution concepts to maximize the possibility of finding sequences with a shared evolutionary history. Less obviously, another benefit of teaching students how the BLAST algorithm works is that it provides an opportunity to illustrate how mathematics functions as a language of biology. Database queries and their tradeoffs (speed versus completeness).It is possible to use case studies from the literature, but the abundance of sequence data present in public databases raises the far more attractive possibility of using searches tailored to a particular course, or, better yet, allowing the students to choose their own examples. ![]() Concepts of molecular evolution (e.g., gene duplication and divergence orthologs versus paralogs) are quite abstract and are best communicated with examples ( Box 1). Recognition of the importance of BLAST to modern life sciences has led to its use in many biology courses, even at the high school level, to introduce students to bioinformatics applications in the life sciences. At the same time, by rendering thinking unnecessary, BLAST is often used suboptimally, with many experienced researchers simply using the default parameters because they do not know how to manipulate them or accepting results with little understanding of their full meaning (or lack thereof). Its speed and ease of use help account for this, with experiments requiring simply submitting a sequence of interest (the query sequence) and waiting a few seconds. BLAST is often the first step in using sequence-based information to design experiments and contextualize experimental results. National Center for Biotechnology Information nt,īLAST (Basic Local Alignment Search Tool, ) is the key bioinformatic tool for sequence comparison and retrieval from databases. The work of CAK at the JGI is under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract number DE-AC02-05CH11231, Lawrence Livermore National Laboratory under contract number DE-AC52-07NA27344.The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.įunding: Curriculum development activities of CAK and KMS are supported in part by a USDA Higher Education Challenge Grant, MOE-2008-02036, as well as NSF MCB-0643713 to KMS. Kerfeld, University of California Berkeley/JGI, United States of AmericaĬopyright: © 2011 Kerfeld, Scott. Citation: Kerfeld CA, Scott KM (2011) Using BLAST to Teach “E-value-tionary” Concepts.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |