FindTarget: software for subtractive genome analysis
FindTarget: software for subtractive genome analysis
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DOI：
10.1099/00221287-147-10-2643
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发表时间：
2001-10-01
期刊：
影响因子：
2.8
通讯作者：
Kunst, F
中科院分区：
文献类型：
--
作者：
Chetouani, F;Glaser, P;Kunst, F
在SICFICO中，消减/差异基因组分析是一种有效的方法来识别属或种特有的基因，或负责独特表型的基因组。通过这种方法，人们可以搜索存在于一组细菌中而不存在于另一组细菌中的基因。已经开发了一个名为FindTarget的软件包，它有一个用户友好的网络界面，以促进差异基因组分析。用户选择要比较的基因组、相似性标准和阈值，以确定一个基因是否在另一个基因组中有对应的基因。这些搜索是基于蛋白质组的BLASTP比较。FindTarget还包括访问序列、有色多重比对、保守蛋白质的系统发育树以及公共注释数据库的链接，这些数据库提供了验证结果的手段。为了说明这一方法，FindTarget搜索可能涉及革兰氏阴性细菌细胞包膜合成特异性的基因。结果表明，大多数已识别的基因都清楚地参与了细胞壁过程，这突显了这种方法的总体力量，特别是FindTarget的力量。
In sifico subtractive/differential genome analysis is a powerful approach for identifying genus- or species-specific genes, or groups of genes that are responsible for a unique phenotype. By this method, one searches for genes present in one group of bacteria and absent in another group. A software package has been developed, named FindTarget, that has a user-friendly web interface to facilitate differential genome analysis. The user chooses the genomes to compare, the similarity criteria and the thresholds to decide if a gene has a counterpart in another genome. The searches are based on BLASTP comparisons of proteomes. FindTarget also includes access to sequences, coloured multiple alignments, phylogenetic trees of conserved proteins and links to public annotated databases which provide a means for validation of the results. To illustrate this approach, a FindTarget search for genes putatively involved in the specificity of cell envelope synthesis of Gram-negative bacteria is presented. The results show that most of the identified genes are clearly involved in cell wall processes, underlining the power of such an approach in general and that of FindTarget in particular.