PipMaker - A Web server for aligning two genomic DNA sequences
PipMaker - A Web server for aligning two genomic DNA sequences
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DOI：
10.1101/gr.10.4.577
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发表时间：
2000-04-01
期刊：
影响因子：
7
通讯作者：
Miller, W
中科院分区：
文献类型：
--
作者：
Schwartz, S;Zhang, Z;Miller, W
PipMaker（http：bio.cse.psu.edu）是一个万维网网站，用于比较两个长DNA序列以鉴定保守片段，并用于产生所得到的比对的信息性高分辨率显示。一种显示是同一性百分比图（pip），其以紧凑且易于理解的形式显示一个序列中的位置和两个序列之间的每个比对区段的相似性程度。沿着水平轴的位置沿着可以用诸如基因的外显子和重复元件的特征来标记，并且颜色可以用于澄清和增强显示。该网站还提供了两个物种中这些片段的位置图（类似于点图）。PipMaker适用于比较任何两个相关物种的基因组序列，尽管可以推断的信息类型（例如，蛋白质编码区和顺式调节元件）依赖于物种分离以来的保守水平和时间以及分化率。基因调控元件通常在1 - 3亿年前分化的物种中作为相似的非编码序列被检测到，例如人类和小鼠，秀丽隐杆线虫和C。或大肠杆菌和沙门氏菌属（Salmonella spp.）PipMaker通过允许两个序列中的一个处于未定向和无序的重叠群中来支持未完成或“工作草案”序列的分析。
PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resulting alignments. One display is a percent identity plot (pip), which shows both the position in one sequence and the degree of similarity for each aligning segment between the two sequences in a compact and easily understandable form. Positions along the horizontal axis can be labeled with features such as exons of genes and repetitive elements, and colors can be used to clarify and enhance the display. The web site also provides a plot of the Locations of those segments in both species (similar to a dot plot). PipMaker is appropriate for comparing genomic sequences from any two related species, although the types of information that can be inferred (e.g., protein-coding regions and cis-regulatory elements) depend on the level of conservation and the time and divergence rate since the separation of the species. Gene regulatory elements are often detectable as similar, noncoding sequences in species that diverged as much as 100-300 million years ago, such as humans and mice, Caenorhabditis elegans and C. briggsae, or Escherichia coli and Salmonella spp. PipMaker supports analysis of unfinished or "working draft" sequences by permitting one of the two sequences to be in unoriented and unordered contigs.