Derivation of transcript patterns by the AltTrans pipeline from AltSplice splice patterns. Each of the gene-transcript alignments from AltSplice is examined for the following: (i) the alignment shows a 3' dangling end on the EST/mRNA; (ii) such a dangling end shows a polyA tail sequence; and (iii) a polyA signal is seen on the gene within a maximum distance of 40 nts 5' to the cleavage position. Transcripts that show these features are grouped in a manner that each class of transcripts possesses the same exon/intron organisation and the same terminating polyA site. Such derived alternate transcript patterns are described as AltTrans transcript patterns. Note: Of the three EST's, that are all grouped under one AltSplice splice pattern, the EST3 does not show a "dangling end" and hence it is not considered further in the construction of AltTrans Transcript Patterns. EST1 and EST2 form two distinct transcript patterns that differ in terminating polyA sites.
Le Texier et al. BMC Bioinformatics 2006 7:169 doi:10.1186/1471-2105-7-169