Create features in Geneious for the predicted exons from geneid. Use the geneid web server ( homepage) to find genes in the genomic DNA fragment. Do the predicted protein coding regions correspond to the EST and BLASTX features that you made?Ĩ. This graph is calculated using the Fickett algorithm.
In Geneious, click on the graphs symbol and select “Protein Coding Prediction”. How many genes are in the Oryza DNA fragment?Ĭan you determine the correct reading frame each exon?ħ. Compare the EST features and the BLASTX features. Select the top 4 or 5 BLAST HSPs and create features on the genomic sequence in Geneious.Ħ. You my try either the nr database or the SwissProt database. Using the Oryza genomic sequence, perform a BLASTX search. In Geneious, create a feature for each HSP from the blast report.ĥ. Record the start and end locations of each HSP.Ĥ. Select the top 5 or 6 ESTs with the best alignments. These alignments should correspond to the parts of the gene that are transcribed (exons and UTRs)ģ. Examine the locations of the alignments on the query sequence. Perform a BLASTN search to the est_others database.Ģ.
Open the link to the Oryza genomic DNA segment above and copy/paste it into Geneious. First, we will align ESTs to the genomic DNA with BLASTN. DNA Sequence for these tutorials: oryza.fasta a segment of genomic DNA from (Oryza sativa).ġ.
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