TABLE OF CONTENTS
[This page does not yet have documentation for all of the tools, but what is here should be correct.]
Fetches pre-computed sequence alignments of the specified genome assemblies (in axt format) that overlap the regions in the selected query. For more details on which alignments are retrieved, see the FAQ.
Computes Pearson's correlation coefficient between two score columns within a single query.
The input must meet the requirements of gtab format, i.e. it must be tab-separated and have chromosome/contig, start position, and end position in the first three columns. Currently this tool does not support multiple scores in a single column, as may happen in some xbed files. The usual way to obtain an input file for this tool is to run the Join operation on two bed queries (or on xbed queries having only a single additional score).
The output is an HTML file reporting the result. As with all tools, this is added to the history. To view the result, select its history item and then choose "Get output".
Plots the distribution of score values in a query.
If the query is in standard BED format (.bed), then the default (i.e., only) score column is used. But if the query is in extended BED format (.xbed), then any of the scores in the file can be chosen. A variety of graph styles and colors are available.
The output is an HTML file referring to a PNG image. As with all tools, this is added to the history. To view the graph, select its history item and then choose "Get output".
Filters a query to find regions above and/or below user-specified score thresholds.
If the query is in standard BED format (.bed), then the default (i.e., only) score column is used. But if the query is in extended BED format (.xbed), then any of the scores in the file can be chosen.
The tool will attempt to show the range of meaningful values for the selected score (if known), for use as a reference when choosing the thresholds. This information is updated via JavaScript when a different .xbed score is selected, so enabling JavaScript in the web browser is recommended.
Computes the reverse complement of an alignment (.axt, .stitch) query. This tool is typically used as a preliminary step to prepare data for the KA/KS tool.
Merges all alignment sets within an alignment (.axt, .stitch) query into one alignment. This tool is typically used as a preliminary step to prepare data for the KA/KS tool.