Genotator: a workbench for sequence annotation

Abstract

Sequencing centers such as the Human Genome Center at LBNL are producing an ever-increasing flood of genetic data. Annotation can greatly enhance the biological value of these sequences. Useful annotations include possible gene locations, homologies to known genes, and gene signal such as promoters and splice sites. Genotator is a workbench for automated sequence annotation and annotation browsing. The back end runs a series of sequence analysis tools on a DNA sequence, handling the various input and output formats required by the tools. Genotator currently runs five different gene-finding programs, three homology searches, and searches for promoters, splice sites, and ORFs. The results of the analyses run by Genotator can be viewed with the interactive graphical browser. The browser displays color-coded sequence annotations on a canvas that can be scrolled and zoomed, allowing the annotated sequence to be explored at multiple levels of detail. The user can view the actual DNA sequence in a separate window; when a region is selected in the map display, it is highlighted automatically in the sequence display, and vice versa. By displaying the output of all of the sequence analyses, Genotator provides an intuitive way to identify the significant regions (for example, probable exons) in a sequence. Users can interactively add personal annotations to label regions of interest. Additional capabilities of Genotator include primer design and pattern searching.

Figure 1

Organization of Genotator.

Figure 2

Genotator directory hierarchy for sequence annotations.

Figure 3

Flowchart showing how sequences are processed by the Genotator back end.

Figure 4

The GUI used to invoke Genotator.

Figure 5

The Genotator browser map display of the annotations on HUMTFPB. The default annotation colors can be seen in the online supplement at http:/cshl.org/gr and are (magenta) NNPP promoter predictions; (red) GenPept hits (using BLASTX). GenPept consists of all the GenBank coding regions translated to amino acids; (orange) EST hits (using BLASTN); (yellow) human repeat sequence hits (using BLASTN); (chartreuse) xpound exon predictions; (green) GeneFinder exon predictions; (turquoise) GRAIL exon predictions; (dark blue) Genie exon predictions; (purple) GenBank CDS (exons); (magenta/red/orange) ORFs (⩾150 bases), colored by frame.

Figure 6

The Genotator browser sequence display showing the sequence of HUMTFPB. The user has clicked on a GenPept BLAST hit in the map display, causing the corresponding sequence region to be highlighted here in gray and red in the sequence display as seen in online suppplement at http://cshl.org/gr.

Figure 8

Annotations on h78_1_c10, indicating a possible new gene associated with the photoreceptor membrane. Color on-line supplement available at http://www.cshl.org/gr.

Figure 7

Preparing to add a personal annotation. The user has selected a region to be annotated and a color for the annotation, and has entered text for the annotation. To add the annotation, they will click “Add Annotation to Map” and/or “Add Annotation to Sequence.”