There are several settings available in the BLAST Graphics view.
- BLAST Layout. You can choose to Gather sequences at top. Enabling this option affects the view that is shown when scrolling horizontally along a BLAST result. If selected, the sequence hits which did not contribute to the visible part of the BLAST graphics will be omitted whereas the found BLAST hits will automatically be placed right below the query sequence.
- Compactness: You can control the level of sequence detail to be displayed:
- Not compact. Full detail and spaces between the sequences.
- Low. The normal settings where the residues are visible (when zoomed in) but with no extra spaces between.
- Medium. The sequences are represented as lines and the residues are not visible. There is some space between the sequences.
- Compact. Even less space between the sequences.
- BLAST hit coloring. You can choose whether to color hit sequences and you can adjust the coloring.
- Coverage: In the Alignment info in the Side Panel, you can visualize the number of hit sequences at a given position on the query sequence. The level of coverage is relative to the overall number of hits included in the result.
- Foreground color. Colors the letters using a gradient, where the left side color is used for low coverage and the right side is used for maximum coverage.
- Background color. Colors the background of the letters using a gradient, where the left side color is used for low coverage and the right side is used for maximum coverage
- Graph. The coverage is displayed as a graph beneath the query sequence (Learn how to export the data behind the graph).
- Height. Specifies the height of the graph.
- Type. The graph can be displayed as Line plot, Bar plot or as a Color bar.
- Color box. For Line and Bar plots, the color of the plot can be set by clicking the color box. If a Color bar is chosen, the color box is replaced by a gradient color box as described under Foreground color.
The remaining View preferences for BLAST Graphics are the same as those of alignments. See section Alignment view preferences.
- Name of sequence. Here is shown some additional information of the sequence which was found. This line corresponds to the description line in GenBank (if the search was conducted on the nr database).
- Score. This shows the bit score of the local alignment generated through the BLAST search.
- Expect. Also known as the E-value. A low value indicates a homologous sequence. Higher E-values indicate that BLAST found a less homologous sequence.
- Identities. This number shows the number of identical residues or nucleotides in the obtained alignment.
- Gaps. This number shows whether the alignment has gaps or not.
- Strand. This is only valid for nucleotide sequences and show the direction of the aligned strands. Minus indicate a complementary strand.
- Query. This is the sequence (or part of the sequence) which you have used for the BLAST search.
- Sbjct (subject). This is the sequence found in the database.
The numbers of the query and subject sequences refer to the sequence positions in the submitted and found sequences. If the subject sequence has number 59 in front of the sequence, this means that 58 residues are found upstream of this position, but these are not included in the alignment.
By right clicking the sequence name in the Graphical BLAST output it is possible to download the full hits sequence from NCBI with accompanying annotations and information. It is also possible to just open the actual hit sequence in a new view.