PMC

The Sequence Similarity Query Tool. In the graphical summary of the Sequence Similarity Query tool, a dendrogram shows the relationships between the sequences in a protein family. A bar graph shows the distribution of members of the protein family within broad taxonomic groupings. The color coding used in the bar graph is also used for the names of the sequences within the dendrogram to indicate the taxonomic grouping.

The Fungal Alignment Viewer. The Fungal Alignment Viewer displays available fungal sequences related to an S.cerevisiae sequence of interest. At the top of the display is a dendrogram showing the relationships between all included sequences. The available sequences are aligned via ClustalW with color coding to indicate conservation (yellow = identical, pink = strong similarity, green = weak similarity). Above the ClustalW alignment is a control menu that allows selection of sequences and type of alignment (protein, ORF DNA, upstream sequence, downstream sequence, ORF DNA + 1 kb up/downstream). When the ‘Align’ button is pressed, the alignment is recomputed according to the user’s selections. Individual sequences present in the alignment are displayed below the ClustalW alignment (not shown here). In the alignment shown, the partial sequence from S.mikatae, available from the sequence selection menu, has not been included so that sequence similarity between the C-terminal portions of the other available sequences can be visualized by ClustalW.