Never-ending stories. Kun-Mao Chao ( 趙坤茂 ) Dept. of Computer Science and Information Engineering National Taiwan University, Taiwan E-mail: [email protected] WWW: http://www.csie.ntu.edu.tw/~kmchao. Part I. Minimum spanning trees. Minimum spanning trees (MST).
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.
FASTA’s Last Stage
Chao, K. -M., Hardison, R. C. and Miller, W. , 1993, Constrained Sequence Alignment, Bulletin of Mathematical Biology, 55: 503-524.
Band Arbitrary boundary lines
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.
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 -Globin Gene Revealed by an Improved Multiple Alignment Program and Functional Analysis, DNA Sequence, 4: 163-176.
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.
Multiple alignment applications
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.
YAMA (Yet Another Multiple Aligner)
Chao, K. -M. and Miller, W. , 1995, Linear-Space Algorithms that Build Local Alignments from Fragments, Algorithmica, 13: 106-134.
falign: Somewhere between FASTA and BLAST
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.
falign + constrained sequence alignment
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.
Fast algorithms for very similar sequences
Chao, K. -M., 1998, “On Computing all Suboptimal Alignments,” Information Sciences, 105: 189-207.
Chao, K. -M., 1999, “Calign: Aligning Sequences with Restricted Affine Gap Penalties,” Bioinformatics, 15: 298-304.
cDNA vs. Genomic sequences
Lin, Y. -L., Jiang, T. and Chao, K. -M., 2002, “Efficient Algorithms for Locating the Length-Constrained Heaviest Segments, with Applications to Biomolecular Sequence Analysis,” Journal of Computer and System Sciences (JCSS), Accepted. (Work done in October, 2001.)
Algorithms for locating a maximum-sum or maximum-average region with length constraints.
Lin, Y. -L., Huang, X., Jiang, T. and Chao, K. -M., 2003, “MAVG: Locating Non-Overlapping Maximum Average Segments in a Given Sequence,” Bioinformatics, January issue. (Work done in April, 2002.)
A tool for locating k-best average regions
Huang, X. and Chao, K. -M., 2003, “A Generalized Global Alignment Algorithm,” Bioinformatics, February issue. (Work done in May, 2002.)
GAP3: Chaining local alignments
(To be continued.)