PipMaker - A Web server for aligning two genomic DNA sequences

PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing tw o long DNA sequences to identify conserved segments and for producing infor mative, high-resolution displays of the resulting alignments. One display i s a percent identity plot (pip), which shows both the position in one seque nce 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 rep etitive 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 b oth species (similar to a dot plot). PipMaker is appropriate for comparing genomic sequences from any two related species, although the types of infor mation that can be inferred (e.g., protein-coding regions and cis-regulator y elements) depend on the level of conservation and the time and divergence rate since the separation of the species. Gene regulatory elements are oft en detectable as similar, noncoding sequences in species that diverged as m uch as 100-300 million years ago, such as humans and mice, Caenorhabditis e legans and C. briggsae, or Escherichia coli and Salmonella spp. PipMaker su pports analysis of unfinished or "working draft" sequences by permitting on e of the two sequences to be in unoriented and unordered contigs.