Detect Elevations and Gaps in Mapped Sequencing Read Coverage
Change the pileup window size
Summarizes pattern-matching results
Collect information regarding the pattern-match
'chunk' long contigs
Classifies partial elevation/gap pattern-matches
Controller function for full elevation/gap pattern-matching
Shrink the width of full elevation and gap patterns
Gene annotation plot
Search for gene annotations on classified contigs/chunks
'chunk' genomes
Detect gene predictions in elevations and gaps
Link pattern-matches on contig/genome chunks
No read coverage pattern
Controller function for partial elevation/gap pattern-matching
Shrink the width of partial elevation and gap patterns
Builds pattern-match vectors
Controller function for pattern-matching
Full elevation/gap pattern translator
Reformat input pileup file
Plot results of ProActive() pattern-matching
ProActive
Detect elevations and gaps in mapped read coverage patterns.
Removes 'NoPattern' classifications from best match list
Automate the detection of gaps and elevations in mapped sequencing read coverage using a 2D pattern-matching algorithm. 'ProActive' detects, characterizes and visualizes read coverage patterns in both genomes and metagenomes. Optionally, users may provide gene annotations associated with their genome or metagenome in the form of a .gff file. In this case, 'ProActive' will generate an additional output table containing the gene annotations found within the detected regions of gapped and elevated read coverage. Additionally, users can search for gene annotations of interest in the output read coverage plots.
Useful links