Gene Identification: Methods and Considerations
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Abstract
This unit introduces readers to some of the more commonly used techniques for gene identification. The author discusses the general problem behind accurately predicting genes in both prefinished and finished sequence data, provides a handson description of programs available in the public domain, and suggests strategies for how to best tackle the prediction problem at various stages of data generation and assembly.This unit introduces readers to some of the more commonly used techniques for gene identification.
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- Gene Identification Methods
- How Well do the Methods Work?
- Strategies and Considerations
- Literature Cited
- Figures
- Tables
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Figure 6.6.1 The central dogma of molecular biology. Proceeding from the DNA through the RNA to the protein level, various sequence features and modifications can be identified that can be used in the computational deduction of gene structure. These include the presence of promoter and regulatory regions, intron‐exon boundaries, and both start and stop signals. Unfortunately, these signals are not always present, and when present may not always be in the same form or context. The reader is referred to the text for greater detail. View Image -
Figure 6.6.2 XGRAIL output obtained using the human BAC clone RG364P16 from 7q31 as the query. The upper window shows the results of the prediction, with the histogram representing the probability that a given stretch of DNA is an exon. The various colored bars in the center represent features of the DNA (e.g., arrows represent repetitive DNA, and vertical bars represent repeat sequences). Exon and gene models, protein translations, and the results of a genQuest search using the protein translation are shown. The reader is referred to UNIT for more details on the interpretation of XGRAIL output. View Image -
Figure 6.6.3 FGENES output obtained using the human BAC clone RG364P16 from 7q31 as the query. The columns, going from left to right, represent the gene number (G), strand (Str), feature (described in the main text), start and end points for the predicted exon, a scoring weight, and start and end points for corresponding open reading frames (ORF‐start and ORF‐end). Each predicted gene is shown as a separate block. Following the tables are protein translations of any predicted gene products. View Image -
Figure 6.6.4 MZEF output obtained using the human BAC clone RG364P16 from 7q31 as the query. The columns, going from left to right, give the location of the prediction as a range of included bases (Coordinates), the probability value (P), frame preference scores (Fr i ), an ORF indicator showing which reading frames are open, and scores for the 3′ splice site, coding regions, and 5′ splice site. View Image -
Figure 6.6.5 GENSCAN output obtained using the human BAC clone RG364P16 from 7q31 as the query. The columns, going from left to right, represent the gene and exon number (Gn.Ex), the type of prediction (Type), the strand on which the prediction was made (S, with + indicating the forward strand and − as the reverse), the beginning and endpoint for the prediction (Begin and End), the length of the prediction (Len), the reading frame of the prediction (Fr), several scoring columns, and the probability value (P). Each predicted gene is shown as a separate block; notice that the third gene has its exons listed in reverse order, reflecting the fact that the prediction is on the reverse strand. Following the tables are the protein translations for each of the three predicted genes. View Image -
Figure 6.6.6 GENSCAN output in graphical form, obtained using the human BAC clone RG364P16 from 7q31 as the query. Optimal and suboptimal exons are indicated, and the initial and terminal exons show the direction in which the prediction is being made (5′ → 3′ or 3′ → 5′). View Image -
Figure 6.6.7 Comparison of GENSCAN with GenomeScan, using the human BRCA1 gene sequence as the query. The GENSCAN prediction (top line) is missing a number of the exons that appear in the annotation for the BRCA1 gene (second line; GenBank L78833), and the GENSCAN prediction is slightly longer than the actual gene at the 5′ end. The inclusion of BLASTX hit information (vertical bars closest to the scale) in GenomeScan produces a more complete and accurate prediction (third line). View Image -
Figure 6.6.8 Sensitivity vs. specificity. In the upper portion of the figure, the four possible outcomes of a prediction are shown: a true positive (TP), a true negative (TN), a false positive (FP), and a false negative (FN). The matrix at the bottom of the figure shows how both sensitivity and specificity are determined from these four possible outcomes, giving a tangible measure of the effectiveness of any gene prediction method. (Figure adapted from Burset and Guigó, , and Snyder and Stormo, .) View Image -
Figure 6.6.9 Annotated output from GeneMachine showing the results of multiple gene prediction program runs. NCBI Sequin is used at the viewer. At the top of the output are shown the results from various BLAST runs (BLASTN vs. DbEST, BLASTN vs. nr, and BLASTX vs. SWISS‐PROT). Towards the bottom of the window are shown the results from the predictive methods (FGENES, GENSCAN, MZEF, and GRAIL 2). Annotations indicating the strength of the prediction are preserved and shown wherever possible within the viewer. Putative regions of high interest would be areas where hits from the BLAST runs line up with exon predictions from the gene prediction programs. View Image
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Literature Cited
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