15.2.1 BLAST hit table

If you chose to return your results in a hit table, each search hit is displayed separately in the document table sorted by bit score. The bit score gives an indication of how good the alignment is; the higher the score, the better the alignment. In general terms, this score is calculated from a formula that takes into account the alignment of similar or identical residues, as well as any gaps introduced to align the sequences.

Search hits can also be sorted by other columns by clicking on the column header. Columns that may be useful to sort by include E-value, Percent Identity, Query Coverage or Grade. E value or “Expect value” represents the number of hits with at least this score that you would expect purely by chance, given the size of the database and query sequence. The lower the E-value, the more likely that the hit is real. The Grade column is a percentage calculated by Geneious by combining the query coverage, e-value and identity values for each hit with weights 0.5, 0.25 and 0.25 respectively. This allows you to sort hits such that the longest, highest identity hits are at the top.

Specifically, Grade = 50 fractionCoverage + 25 (maximum(0,1 eV alue∕1020)) + 25 (maximum(0,(percentIdentity minGradedIdentity)(100 minGradedIdentity))) , where minGradedIdentity is 50 for nucleotide and 25 for protein sequences


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Figure 15.2: BLAST Complete



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Figure 15.3: Document After Full Sequence Download


You can also download the full database sequence that corresponds to a BLAST hit. To retrieve the full sequence select a BLAST alignment and go to File Download Documents or click the Download Full Sequence(s) button located above the viewer tabs. The full sequence will be available in the Sequence View tab once the download has completed and the region that matches the query sequence will be annotated as BLAST Hit (see Figure 15.3 ). In addition the annotations from the full sequence will be transferred over to the BLAST alignment and can be viewed in Alignment view.