Softwares

Software List

The software packages that I made or I was involved in are introduced in this page. Please contact me to know more about them.

FastHinge 1.0

The FastHinge 1.0 is a very fast hinge prediction program that predicts hinge positions by comparing already-aligned two flexible structures. Only the Windows XP/SunOS 5.8 executable files are provided.

Tetsuo Shibuya, Fast Hinge Detection Algorithms for Flexible Protein Structures, IEEE/ACM Transactions on Computational Biology and Bioinformatics, to appear. (preprint)
Tetsuo Shibuya, Efficient Substructure RMSD Query Algorithms, Journal of Computational Biology, Vol. 14, No. 9., 2007, pp. 1201-1207. (journal site) (preprint)

GeoST

GeoST is a program for indexing protein structures based on a data structure called the `geometric suffix tree'. The data structure enables searching for similar substructures in protein databases, where `similar' means RMSD is within some bound. It enumerates all the substructures whose RMSD to the query is within a given bound.

Tetsuo Shibuya, Efficient Substructure RMSD Query Algorithms, Journal of Computational Biology, Vol. 14, No. 9., 2007, pp. 1201-1207. (journal site) (preprint)
Tetsuo Shibuya, Prefix-Shuffled Geometric Suffix Tree, Proc. 14th String Processing and Information Retrieval Symposium (SPIRE 2007), LNCS 4726, 2007, pp. 300-309. (PDF file)
Tetsuo Shibuya, Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures, Combinatorial Pattern Matching 2006 (CPM 2006), LNCS 4009, Barcelona, July 5-7, 2006, pp. 84-93. (PDF file)

BDGF

BDGF (BioDictionary Gene Finder) is a gene finding tool based on a very large protein pattern database called BioDictionary. The server is located at Bioinformatics and Pattern Discovery Grpup at IBM Watson Research Center.

References

Tetsuo Shibuya and Isidore Rigoutsos, Dictionary-driven Prokaryotic Gene Finding, Nucleic Acids Research, Vol. 30, pp. 2710-2725, 2002.
Tien Huynh, Isidore Rigoutsos, Laxmi Parida, Daniel Platt and Tetsuo Shibuya, The IBM Bioinformatics Group Web Server - Tools and Content, Nucleic Acids Research, Vol. 31, No. 13, pp. 3645-3650, 2003.
Eain Murphy, Isidore Rigoutsos, Tetsuo Shibuya, and Thomas Shenk, Re-evaluation of human cytomegalovirus coding potential, Proceedings of the National Academy of Sciences, Vol. 100, No. 23, pp. 13585-13590, November 11, 2003.

CLUSPA

CLUSPA is an accurate and fast tool for clustering cDNA sequences and determining alternative splice variant candidates without mapping to the genome sequence. Unlike BLAST or FASTA-based tools, CLUSPA considers splicing sites when comparing sequences and therefore achieves more accurate clustering. You need an account of OBIGrid (free) to log in to this server.

References

Tetsuo Shibuya, Hisashi Kashima and Akihiko Konagaya, Accurate cDNA Clustering Algorithm based on Spliced Sequence Alignment. Bioinformatics, Vol. 20, pp. 29-39, 2004.

FMA

FMA is a multiple alignment tool for obtaining alternative solutions to the optimal sum-of-pairs multiple alignment by enumerating suboptimal alignments and doing parametric analysis.

References

Tetsuo Shibuya and Hiroshi Imai, New Flexible Approaches for Multiple Sequence Alignment, Journal of Computational Biology, Vol. 4, No. 3, Mary Ann Liebert, Inc., pp. 385-413, 1997.

MCCM

MCCM is a cDNA mapping program based on suffix trees. - But not in public.

References

Tetsuo Shibuya and Igor Kurochkin, Match Chaining Algorithms for cDNA Mapping. Algorithms in Bioinformatics (WABI'03), LNCS 2182, Budapest, September 2003, pp. 462-473.

Super IF-MAP

Super IF-MAP is a GIS software package of IBM which I was involved in when I was with IBM..

References

Tetsuo Shibuya, Computing the n x m Shortest Paths Efficiently, the ACM Journal of Experimental Algorithmics, ISSN 1084-6654, Vol. 5, No. 9, 2000.

PayPerClick

PayPerClick is a WWW account server software program developed at IBM which I was involved in when I was with IBM.

References

Hiroshi Kawazoe, Tetsuo Shibuya, and Takeshi Tokuyama, Optimal on-line algorithms for an electronic commerce money distribution system, Algorithmica, Vol. 33, pp. 287-299, March 25, 2002.