Ladunga Istvan
Departments of Statistics, Biochemistry, and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska.
Curr Protoc Bioinformatics. 2017 Jun 27;58:3.3.1-3.3.25. doi: 10.1002/cpbi.29.
The Basic Local Alignment Search Tool (BLAST) is the first tool in the annotation of nucleotide or amino acid sequences. BLAST is a flagship of bioinformatics due to its performance and user-friendliness. Beginners and intermediate users will learn how to design and submit blastn and Megablast searches on the Web pages at the National Center for Biotechnology Information. We map nucleic acid sequences to genomes, find identical or similar mRNAs, expressed sequence tag, and noncoding RNA sequences, and run Megablast searches, which are much faster than blastn. Understanding results is assisted by taxonomy reports, genomic views, and multiple alignments. We interpret expected frequency thresholds, biological significance, and statistical significance. Weak hits provide no evidence, but indicate hints for further analyses. We find genes that may code for homologous proteins by translated BLAST. We reduce false positives by filtering out low-complexity regions. Parsed BLAST results can be integrated into analysis pipelines. Links in the output connect to Entrez and PubMed, as well as structural, sequence, interaction, and expression databases. This facilitates integration with a wide spectrum of biological knowledge. © 2017 by John Wiley & Sons, Inc.
基本局部比对搜索工具（BLAST）是核苷酸或氨基酸序列注释中的首个工具。由于其性能和用户友好性，BLAST是生物信息学的旗舰工具。初学者和中级用户将学习如何在美国国立生物技术信息中心的网页上设计并提交blastn和Megablast搜索。我们将核酸序列映射到基因组，找到相同或相似的mRNA、表达序列标签和非编码RNA序列，并运行比blastn快得多的Megablast搜索。分类学报告、基因组视图和多重比对有助于理解结果。我们解读预期频率阈值、生物学意义和统计学意义。弱匹配无证据，但可为进一步分析提供线索。我们通过翻译后的BLAST找到可能编码同源蛋白的基因。我们通过过滤低复杂度区域来减少假阳性。解析后的BLAST结果可整合到分析流程中。输出中的链接可连接到Entrez和PubMed，以及结构、序列、相互作用和表达数据库。这便于与广泛的生物学知识进行整合。© 2017约翰威立父子出版公司
