By Wolfsberg Tyra G., Wetterstrand Kris A., Guyer Mark S., Collins Francis S., Baxevanis Andreas D.
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Additional resources for A user's guide to the human genome
5), which can be accessed in a number of ways; for example, by clicking on the View Evidence box for a transcript on the GeneView (Fig. 10). Another good starting point for visualizing alternatively spliced transcripts is the NCBI’s Model Maker (follow the mm link in Fig. 2). The Model Maker displays putative exons from mRNAs, ESTs and gene predictions that align with the genome. Users can select individual exons from these alignments and build a customized gene model. As the Model Maker displays the nucleotide sequence of the model along with its three-frame translation, the effects of adding, modifying or deleting exons can be quickly evaluated.
Clicking on Text Search, on the left, brings the user to the search page; for this search, type ‘HMG Box’ into the text box and hit Search. Three hits are returned (Fig. 6). For purposes of this example, follow the link from the first hit, for high mobility group proteins HMG1 and HMG2 (IPR000135). The resulting InterPro summary page (Fig. 7) provides information on the function, intracellular location and, most importantly, metabolic role of this particular protein within the cell, in an executive summary format.
The Human mRNAs from Genbank track shows alignments between human mRNAs in GenBank and the genome sequence. The Spliced ESTs and Human EST tracks show the alignment of ESTs from GenBank against the genome. Because ESTs usually represent fragments of transcribed genes, there is high likelihood that an EST corresponds to an exonic region. edu/cgi-bin/RepeatMasker). It is customary to remove or ‘mask’ these elements before applying a gene prediction method to a nucleotide sequence. Returning to the example shown in Fig.