項目符號 band
項目符號 Chao, K.-M., Pearson, W. R. and Miller, W., 1992, Aligning Two Sequences within a Specified Diagonal Band, Computer Applications in the Biosciences (CABIOS, now Bioinformatics), 8: 481-487.
項目符號 region
項目符號 Chao, K.-M., Hardison, R. C. and Miller, W., 1993, Constrained Sequence Alignment, Bulletin of Mathematical Biology, 55: 503-524.
項目符號 robust
項目符號 Chao, K.-M., Hardison, R. C. and Miller, W., 1993, Locating Well-Conserved Regions within a Pairwise Alignment, Computer Applications in the Biosciences (CABIOS, now Bioinformatics), 9: 387-396.
項目符號 yama
項目符號 Hardison, R. C., Chao, K.-M., Adamkiewicz, M., Price, D., Jackson, J., Zeigler, T., Stojanovic, N. and Miller, W., 1993, Positive and Negative Regulatory Elements of the Rabbit Embryonic e-Globin Gene Revealed by an Improved Multiple Alignment Program and Functional Analysis, DNA Sequence, 4: 163-176.
項目符號 Hardison, R. C., Chao, K.-M., Schwartz, S., Stojanovic, N., Ganetsky, M. and Miller, W., 1994, Globin Gene Server: A Prototype E-Mail Database Server Featuring Extensive Multiple Alignments and Data Compilation for Electronic Genetic Analysis, Genomics,  21: 344-353.
項目符號 Chao, K.-M., Hardison R. C. and Miller, W., 1994, Recent Developments in Linear-Space Alignment Methods: a Survey, Journal of Computational Biology, 1: 271-291.
項目符號 sub
項目符號 Chao, K.-M., 1994, Computing All Suboptimal Alignments in Linear Space, Combinatorial Pattern Matching '94, Lecture Notes in Computer Science 807, 31-42, California, USA.
項目符號 falign
項目符號 Chao, K.-M. and Miller, W., 1995, Linear-Space Algorithms that Build Local Alignments from Fragments, Algorithmica, 13: 106-134.
項目符號 sim2
項目符號 Chao, K.-M., Zhang, J., Ostell, J. and Miller, W., 1995, A Local Alignment Tool for Very Long DNA Sequences, Computer Applications in the Biosciences (CABIOS, now Bioinformatics),  11: 147-153.
項目符號 sim3
項目符號 Chao, K.-M., Zhang, J., Ostell, J. and Miller, W., 1997, A Tool for Aligning Very Similar DNA sequences, Computer Applications in the Biosciences (CABIOS, now Bioinformatics),  13: 75-80.
項目符號 calign
項目符號 Chao, K.-M., 1999, “Calign: Aligning Sequences with Restricted Affine Gap Penalties,” Bioinformatics, 15: 298-304.

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