Rambaldi Davide, Guffanti Alessandro, Morandi Paolo, Cassata Giuseppe
IFOM-FIRC Institute of Molecular Oncology Foundation, Milan, Italy.
BMC Bioinformatics. 2005 Dec 1;6 Suppl 4(Suppl 4):S22. doi: 10.1186/1471-2105-6-S4-S22.
NemaFootPrinter (Nematode Transcription Factor Scan Through Philogenetic Footprinting) is a web-based software for interactive identification of conserved, non-exonic DNA segments in the genomes of C. elegans and C. briggsae. It has been implemented according to the following project specifications:a) Automated identification of orthologous gene pairs. b) Interactive selection of the boundaries of the genes to be compared. c) Pairwise sequence comparison with a range of different methods. d) Identification of putative transcription factor binding sites on conserved, non-exonic DNA segments.
Starting from a C. elegans or C. briggsae gene name or identifier, the software identifies the putative ortholog (if any), based on information derived from public nematode genome annotation databases. The investigator can then retrieve the genome DNA sequences of the two orthologous genes; visualize graphically the genes' intron/exon structure and the surrounding DNA regions; select, through an interactive graphical user interface, subsequences of the two gene regions. Using a bioinformatics toolbox (Blast2seq, Dotmatcher, Ssearch and connection to the rVista database) the investigator is able at the end of the procedure to identify and analyze significant sequences similarities, detecting the presence of transcription factor binding sites corresponding to the conserved segments. The software automatically masks exons.
This software is intended as a practical and intuitive tool for the researchers interested in the identification of non-exonic conserved sequence segments between C. elegans and C. briggsae. These sequences may contain regulatory transcriptional elements since they are conserved between two related, but rapidly evolving genomes. This software also highlights the power of genome annotation databases when they are conceived as an open resource and the possibilities offered by seamless integration of different web services via the http protocol.
The program is freely available at http://bio.ifom-firc.it/NTFootPrinter.
NemaFootPrinter（通过系统发育足迹法扫描线虫转录因子）是一款基于网络的软件，用于交互式识别秀丽隐杆线虫和briggsae线虫基因组中保守的非外显子DNA片段。它是根据以下项目规范实现的：a）自动识别直系同源基因对。b）交互式选择要比较的基因边界。c）使用一系列不同方法进行成对序列比较。d）识别保守的非外显子DNA片段上的假定转录因子结合位点。
从秀丽隐杆线虫或briggsae线虫的基因名称或标识符开始，该软件根据来自公共线虫基因组注释数据库的信息识别假定的直系同源物（如果有的话）。研究人员随后可以检索这两个直系同源基因的基因组DNA序列；以图形方式可视化基因的内含子/外显子结构和周围的DNA区域；通过交互式图形用户界面选择这两个基因区域的子序列。使用生物信息学工具箱（Blast2seq、Dotmatcher、Ssearch并连接到rVista数据库），研究人员在该过程结束时能够识别和分析显著的序列相似性，检测与保守片段相对应的转录因子结合位点的存在。该软件会自动屏蔽外显子。
该软件旨在为有兴趣识别秀丽隐杆线虫和briggsae线虫之间非外显子保守序列片段的研究人员提供一个实用且直观的工具。这些序列可能包含调控转录元件，因为它们在两个相关但快速进化的基因组之间是保守的。该软件还突出了基因组注释数据库作为开放资源时的强大功能，以及通过http协议无缝集成不同网络服务所提供的可能性。
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