MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences
MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences
复制标题
DOI：
10.1093/bioinformatics/btp682
复制
发表时间：
2010-02-15
期刊：
影响因子：
5.8
通讯作者：
Bergelson, Joy
中科院分区：
文献类型：
--
作者：
Horton, Matthew;Bodenhausen, Natacha;Bergelson, Joy
动机：我们已经创建了一套基于Java的软件，以更好地为DNA序列提供分类分配。我们预计，该计划将是有用的原生生物学家，病毒学家，真菌学家和其他微生物生态学家。该程序依赖于NCBI实用程序，包括BLAST软件和分类学数据库，并且易于在命令行操作，以指定BLAST候选的查询覆盖率或百分比同一性要求;其他选项包括为八个主要分类等级（域，王国，门......）中的每一个设置最小共识要求（%）的能力。以及当最高命中缺乏分类学分类时是否考虑较低得分的候选。
Motivation: We have created a suite of Java-based software to better provide taxonomic assignments to DNA sequences. We anticipate that the program will be useful for protistologists, virologists, mycologists and other microbial ecologists. The program relies on NCBI utilities including the BLAST software and Taxonomy database and is easily manipulated at the command-line to specify a BLAST candidate's query-coverage or percent identity requirements; other options include the ability to set minimal consensus requirements (%) for each of the eight major taxonomic ranks (Domain, Kingdom, Phylum,...) and whether to consider lower scoring candidates when the top-hit lacks taxonomic classification.