The following videos show aspects of sequence assembly using Assembler (Note: if you experience jerky playback, click pause and wait until the video downloads fully before playback).
Reference Alignment with Bowtie
MacVector 10.5 allows you to align cDNA clones against a corresponding genomic sequence and automatically identify the introns and exons. Actual splice sites at ambiguous junctions are determined using the standard GT..AG intron rule. Once identified you can quickly save each intron or exon as a feature on the parental sequence.