Unit

UNIT 3.6 Constructing and Refining Multiple Sequence Alignments with PileUp, SeqLab, and the GCG Suite

  1. Steven M. Thompson

Published Online: 1 FEB 2003

DOI: 10.1002/0471250953.bi0306s00

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Thompson, S. M. 2003. Constructing and Refining Multiple Sequence Alignments with PileUp, SeqLab, and the GCG Suite. Current Protocols in Bioinformatics. 00:3.6:3.6.1–3.6.73.

Author Information

  1. Florida State University, Tallahassee, Florida

Publication History

  1. Published Online: 1 FEB 2003
  2. Published Print: JAN 2003

Abstract

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.