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**** Tools used by Imagene ****

• Download FASTA
• FASTA manual

• Paper Reference:

     Huang, X., Madan, A. 
     "CAP3: A DNA Sequence Assembly Program."
     Genome Research (1999) 9: 868-877.
  

• The makers of PGA and CAP (Paracel) are no longer in business.

• Paper Reference(s):

     Huang, X., Miller, W.
     "A Time-Efficient, Linear-Space Local Similarity Algorithm."
     Advances in Applied Mathematics (1991) 12:337-357.
  
     Huang, X., Hardison, R. C., Miller, W.
     "A Space-Efficient Algorithm for Local Similarities."
     Computer Applications in the Biosciences" (1990) 6:373-381.
  

• Home site of makers of SIM
• SIM - Local similarity program
• Home Page of SIM and CAP author: Xiaoqui Huang

• Paper Reference

     Zhang, Z., Schwartz, S., Wagner, L. Miller, W.
     "A greedy algorithm for aligning DNA sequences."
     J. Computational Biology (2000) 7:203-214.
  

• Why use the BLAST Program?
• Home Page of BLAST Author: Webb Miller
• MegaBLAST Search Tool

• Paper Reference

     Altschul, Stephen F., Warren Gish  Webb Miller, Eugene W. Myers, and David J. Lipman .
     "Basic Local Alignment Search Tool."
     J. Molecular Biology (1990) 215:403-410
  

• BLAST Home Page

• RepeatMasker at University of Washington

**** Other clustering Algorithms ****

• Unigene Build Procedure
• ClustalW
• PileUp
• Dialign

**** Other Web Based Sequence Alignment Tools ****

• BCM Search Launcher: Pairwise Sequence Alignment