Products:
　VHMPT　VACPS　FLASH　OPAAS　UM method for SNP mapping　HaploScape　UM method for synteny mapping
　Foldzilla　PROPEAT　HMDEG

• VHMPT
  VHMPT is a graphical Viewer and editor for Helical Membrane Protein Topologies.
  It can automatically generate a schematic 2D topology for a protein with transmembrane helices.
  
  Lin, W.-J. and Hwang, M.-J. (1998) VHMPT : a graphical viewer and editor for Helical Membrane Protein Topologies. Bioinformatics, 14, 866-868
  
  
• VACPS
  VACPS is a graphical interface for Viewing Amino-acid Conservation on Protein Structures. VACPS allows users to identify and visualize highly conserved or variable structural regions of a protein. The extent of conservation (conservation score) for each aligned position was computed based on an alignment of multiple sequences or multiple structures according to a scheme described in [1, 2].  The computed conservation score was color-coded into 10 different but contiguous colors going from blue to white then to red, representing, in that order, more and more conserved residues (positions). VACPS interfaces with RasMol [3] for displaying and manipulating the three dimensional structures of proteins.

  [1] W.J. Lin and M.J. Hwang. 1998. VHMPT: a graphical viewer and editor for Helical Membrane Protein Topologies. Bioinformatics 14: 866-868.
  [2] Y.S. Cheng, T.K. Tang and M.J. Hwang. 1999. Amino Acid Conservation abd Clinical Severing of Human Glucose-6-phosphate Dehydrogenase Mutations. J. Biomed.Sci. 6: 106-114.
  [3] R. Sayle and E. James Milner-White.1995. "RasMol: Biomolecular graphics for all", Trends in Biochemical Sciences (TIBS). 20: 374.

  
  
• FLASH
  FLASH - a Fast aLignment Algorithm for finding Structural Homology of proteins.
  FLASH is a fast protein structure comparison program that finds both optimal and alternative alignments.
  
  
  Edward S.C. Shih and Ming-Jing Hwang. 2003. Protein structure comparison by probability-based matching of secondary structure elements Bioinformatics 19: 735-741.
  (Supplement materials.[PDF] )
  (Source code.[C++] Any question about the code, please contact Edward S.C. Shih )
  
  
  
• OPAAS
  OPAAS is a structure comparison method for finding Optimal, Permuted and other Alternative Alignments of protein Structures. It is a modified version of FLASH. OPAAS differs from FLASH mainly in the expanded capability to find not only topological but non-topological (permuted) alignments of protein structures. (Shih & Hwang, Proteins: Structure, Function and Bioinformatics (in press) )
  (Source code.[C++] Any question about the code, please contact Edward S.C. Shih )
  
  
  
• UM method for SNP mapping
  This is a fast, sequence alignment-free and genome-based sequence mapping method. Read a Genome Techology story on this work.
  Leslie Y.Y. Chen, Szu-Hsien Lu, Edward S.C. Shih, and Ming-Jing Hwang. 2002. "Single Nucleotide Polymorphism Mapping Using Genome-Wide Unique Sequences." Genome Research 12: 1106-1111.
  
  
• HaploScape
  HaploScape is a database of genome-wide gene-based haplotype sets derived from a cross-referencing of human dbSNP (database of human Single Nucleotide Polymorphisms records) and dbEST (database of human Expressed Sequence Tag sequences).
  (Leslie Y.Y. Chen, Szu-Hsien Lu, Richie Gan, Austin W.T. Chiang, and Ming-Jing Hwang, submitted)
  
  
• UM method for synteny mapping
  This is a fast, sequence alignment-free method for mapping evolutionary conserved segments between two large genomes.
  Ben-Yang Liao, Yu-Jung Chang, Jan-Ming Ho, and Ming-Jing Hwang. 2004. "The UniMarker (UM) Method for Synteny Mapping of Large Genomes." Bioinformatics (in press).
  
  
• Foldzilla
  Foldzilla is a database of fold-specific structural motifs. It identifies structural motifs in uploaded protein structures, and provides users with curated functional annotation.
  *Ta-tsen Soong, *Cheng-Yu Chen, Ming-Jing Hwang. 2004. Conserved Local Structural Motifs for Functional Annotation of Protein Families. (in preparation)
  * these are joint first authors.
  
  
• PROPEAT
  PROPEAT is a database pf PROtein internal rePEATs identified by performing a one-against-self comparison on all SCOP90 (1.55 release) structures using OPAAS. Currently, 401 internal repeat-containing domains from 96 SCOP folds were manually catalogued into four types of repeats, spiral (solenoid), circular, irregular and duplicate. (Suen et al., in preparation)
  
  
• HMDEG
  A database for Human and Mouse Differentially Expressed Genes, constructed by statistical analysis of EST (expressed sequence tags) database (dbEST).
  
  
• A tutorial for Homology Modeling [doc]
  A tutorial about homology modeling in Chinese.