Constructing and refining multiple sequence alignments with PileUp, SeqLab, and the GCG suite.

This unit discusses how the Accelrys GCG Wisconsin Package SeqLab graphical user interface can be used to align, annotate, analyze, and export into alternative formats, multiple biological sequence data. The emphasis is on discovering and recognizing common elements within the dataset. The GCG programs, or implementations of public domain programs thereof, investigated include: LookUp, PileUp, PlotSimilarity, FASTA, Motifs, MEME/MotifSearch, the Profile Package, the HMMER Package, PAUPSearch, and ToFastA. ReadSeq, a non-GCG, public domain program is also used.