A pip showing human chromosome 22 in the region associated with velocardiofacial syndrome aligned with the orthologous region in mouse. A 60-kb segment surrounding the CDC45L and CLDN5 genes illustrates the alignments and annotations on a pip. Each aligning segment is displayed as a series of horizontal lines whose positions correspond to the first sequence used in the alignment. The aligning segments are drawn according to their percent identity, which is shown on the vertical axis from 50% to 100%. A number of optional annotation files allow a user to augment the information content of the display. For instance, the names of genes and their direction of transcription is part of the exons file format. An underlay file specifies what color to draw genomic features such as exons (e.g., light blue), introns (e.g., light yellow), UTRs (e.g., light orange), and conserved noncoding regions (e.g., shades of red). An annotations file provides colored, horizontal lines above the alignment that are hyperlinks in the PDF file and provide direct links to relevant Internet sites—e.g., appropriate PubMed citation(s) for the gene (red), the LocusLink entry for the gene (blue), or a protein sequence from GenBank (green). The bookmarks along the left side provide links to compiled information about the various genes and other annotations describing the comparative analysis of the sequences. The bookmarks represent a much larger region than that shown in the image.

Illustration of the PipMaker options (A) Show All Matches, (B) Chaining, and (C) Single Coverage. The human -globin gene locus contains a family of duplicated genes which, when aligned to the orthologous region in mouse, shows matches to multiple family members in the mouse globin locus. The option to Show All Matches reveals extensive sequence similarity between globin gene clusters in human and mouse sequences (panel A, from left to right: dot plot of the extended genomic region and the pip of the human -globin gene, HBD). In addition, a cluster of related olfactory receptor genes surrounds the globin locus in both species and creates the checkerboard pattern. The Chaining option reduces the amount of aligning sequence by showing alignments of sequences that appear in the same relative order between the two species (panel B, leftmost box). For this reason, most of the ORGs disappear. One aligning segment is identified for each human globin gene and multiple hits are removed from the pip (panel B, rightmost box). The Single Coverage option identifies the highest-scoring alignments and allows any position in the first sequence to align only once to the second sequence. Therefore, no alignments are in the same vertical space, although they may appear to be very close if the display is of insufficient resolution. In the globin locus, several genes are most similar to the same sequence in the mouse locus (see panel C, leftmost and middle boxes) and appear on the same horizontal line. The pip (panel C, rightmost box) shows more alignments than with the Chaining option because the best match is not restricted to being in the same relative order along the two sequences.

Alternate format for repeats file.

An example of an underlay file which refers to Figure 10.2.7.

An example of a line in the body of an underlay file used to paint just the upper or lower half of a region by using a + or - sign.

A sample annotation entry for the body of an annotation file for Advanced PipMaker.

Icons used in a pip that represent features in a genomic sequence, such as exons, repeats, and CpG islands.

The traditional textual form of alignment output.

Putative coding sequence from optional Analysis of Exons output.

A sample listing of the exon positions for Analysis of Exons output (analogous to Fig. 10.2.17) when the second sequence file contains multiple contigs.

An example of a second sequence consisting of two segments separated by 100 Ns, which is then is treated as shown in Figure 10.2.23.

Example messages from a PDF file with embedded contig names.