PipMaker is a web server for aligning two genomic DNA sequences and identifying conserved segments. It provides a percent identity plot (pip) that shows the position and similarity of aligning segments in a compact and understandable format. The server also includes a dot plot to display segment positions in both species. PipMaker is suitable for comparing sequences from related species, even when one sequence is incomplete. It supports analysis of unfinished sequences by allowing one sequence to be in unoriented and unordered contigs. The availability of complete microbial genomes and the sequencing of human and mouse genomes has driven a revolution in biological sciences. Comparative analysis of genomic sequences is a powerful tool for interpreting genomic information, helping to identify protein-coding regions, regulatory signals, and understand genome evolution. However, existing gene-finding methods have limitations, especially for alternatively spliced genes and sequences with sequencing errors. Interspecies alignments can improve exon assignment accuracy. Finding gene regulatory elements is more challenging due to their small size and low sequence specificity. However, highly conserved noncoding regions can be reliable guides to regulatory elements. PipMaker provides tools for efficient identification of coding and regulatory elements through comparative analysis. It uses BlastZ for alignments and offers various output formats, including pips, dot plots, and textual alignments. PipMaker is useful for finding exons and regulatory elements in mammalian, nematode, and bacterial sequences. It can compare a completed sequence from one species with an incomplete sequence from another. The server allows for the annotation of functional or structural features along the axes of the plots. Examples include the identification of exons and regulatory elements in human, mouse, and nematode sequences. PipMaker also helps distinguish protein-coding regions from untranslated regions by showing differences in percent identity. It reveals candidates for regulatory elements in noncoding regions, which are often conserved in other species. The server can handle large sequences and provides options for removing duplicate alignments, such as chaining and single coverage. The server is a valuable tool for functional genomics, aiding in the analysis of genomic sequences and the generation of hypotheses about gene function. It supports the identification of conserved noncoding sequences and regulatory elements, which are important for understanding gene regulation. PipMaker is an automated server that provides a compact, high-resolution display of alignments, making it a useful resource for genomic research.PipMaker is a web server for aligning two genomic DNA sequences and identifying conserved segments. It provides a percent identity plot (pip) that shows the position and similarity of aligning segments in a compact and understandable format. The server also includes a dot plot to display segment positions in both species. PipMaker is suitable for comparing sequences from related species, even when one sequence is incomplete. It supports analysis of unfinished sequences by allowing one sequence to be in unoriented and unordered contigs. The availability of complete microbial genomes and the sequencing of human and mouse genomes has driven a revolution in biological sciences. Comparative analysis of genomic sequences is a powerful tool for interpreting genomic information, helping to identify protein-coding regions, regulatory signals, and understand genome evolution. However, existing gene-finding methods have limitations, especially for alternatively spliced genes and sequences with sequencing errors. Interspecies alignments can improve exon assignment accuracy. Finding gene regulatory elements is more challenging due to their small size and low sequence specificity. However, highly conserved noncoding regions can be reliable guides to regulatory elements. PipMaker provides tools for efficient identification of coding and regulatory elements through comparative analysis. It uses BlastZ for alignments and offers various output formats, including pips, dot plots, and textual alignments. PipMaker is useful for finding exons and regulatory elements in mammalian, nematode, and bacterial sequences. It can compare a completed sequence from one species with an incomplete sequence from another. The server allows for the annotation of functional or structural features along the axes of the plots. Examples include the identification of exons and regulatory elements in human, mouse, and nematode sequences. PipMaker also helps distinguish protein-coding regions from untranslated regions by showing differences in percent identity. It reveals candidates for regulatory elements in noncoding regions, which are often conserved in other species. The server can handle large sequences and provides options for removing duplicate alignments, such as chaining and single coverage. The server is a valuable tool for functional genomics, aiding in the analysis of genomic sequences and the generation of hypotheses about gene function. It supports the identification of conserved noncoding sequences and regulatory elements, which are important for understanding gene regulation. PipMaker is an automated server that provides a compact, high-resolution display of alignments, making it a useful resource for genomic research.