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Glossary

• Redundant ESTs (span) 2-D representation of the ESTs (span). The set presented is redundant that means it uses all the available ESTs for constructing the plot. This includes those ESTs with high sequence homology to more than one genomic location
• Non redundant ESTs (span) 2-D representation of the ESTs (span). The set presented is non redundant. An EST is used just in case it has a unique location in the genome. This kind of representation is very appropriate for detecting alternative 3'UTR endings
• Redundant ESTs (no span) 2-D representation of the ESTs (non span alignment). The set presented is redundant. that means it uses all the available ESTs for constructing the plot. This includes those ESTs with high sequence homology to more than one genomic location. It is useful for detecting exons, alternative splicing
• Clusters with PAS (crosses, see the graph) the set of EST clusters (predictions) that have a Polyadenylation signal in range (10-30nt upstream the cleavage)
• Clusters EST Ends detected in the genomic range. The high of the bar shows how many ESTs ends there. The width of the bar shows the corresponding width of the EST cluster
• Peaks rough ends detected by the algorithm (see the manuscript). The higher the line (see plot), the greater the number of ESTs ending there
• EST related to clusters a 1-D classical representation of the ESTs related to the clusters (non Redundant, span)
• All PAS all the valid polyadenylation signals
• RefSeq the annotated RefSeq in the range (NM_*)
• Report a plain text that describes the plot in detail
• Baseline in zero, for the sake of clarity

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