|
Databases
|
Reference
|
| After GeneBank |
Annotated-Feature Extractor from GenBank |
| BioinfoArchive |
An online data archive of biological data sets |
| dbPTM |
Lee T. Y. et al. dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res. 2006 Jan 1;34(Database
issue):D622-7. |
| FlyDPI |
Lin C.Y. et al. Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology. BMC Bioinformatics. 2006 Dec
18;7 Suppl 5:S18. |
| GPDB |
Genome Profile Database |
| hp-DPI |
Lin C.Y. et al. hp-DPI: Helicobacter pylori database of protein interactomes--embracing experimental and inferred interactions.
Bioinformatics. 2005 Apr 1;21(7):1288-90. Epub 2004 Oct 28. |
| HPSG |
Structural Genomics Databases of Helicobacter pylori |
| iGenome |
A database index for the genome summarized information |
| KPSG |
Structural Genomics Databases of Klebsiella pneumoniae |
| RegRNA |
Huang H. Y. et al. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res. 2006 Jul 1;34(Web
Server issue):W429-34 |
| SM |
Structural Genomics Databases of Stenotrophomonas maltophili |
| SNP |
SNP value-added database |
| SSDB |
Disulfide Proteins Database |
| TAG |
Chan H.H. et. al. TAG: a comprehensive database for cancer research. (2007) Nucleic Acids Research Molecular Biology Database Collection #
922. |
| The BEST |
Chen K.F. et. al. Transcriptional repression of human cad gene by hypoxia inducible factor-1. (2005) Nucleic Acids Research 33(16):5190-5198. |
| TPMD |
Chang Y.H. et al. TPMD: a database and resources of microsatellite marker genotyped in Taiwanese populations. Nucleic Acids Research, 2005,
Vol. 33, Database issue D174-D177. |
| XCC |
Structural Genomics Databases of Xanthomonas campestris |
|
Tools
|
Reference
|
| 3D-BLAST |
Yang J.M. et al.?Protein structure database search and evolutionary classification. Nucleic Acids Res. 2006 Aug 2;34(13):3646-59. |
| CELLO |
Yu C.S. et al.?Prediction of protein subcellular localization. Proteins. 2006 Aug 15;64(3):643-51. |
| Chameleon Sequence Finder |
Retrive a small peptide fragment sequence from a collection of PDB sequences |
| CPSARST |
Lo W.C. et al.?CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships.
Genome Biol. 2008 Jan 18;9(1):R11. |
| ENACE System |
Chen F.C. et al.?Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome
comparisons in human, mouse and rat. BMC Bioinformatics. In press, 2006. |
| ESTviewer |
Chen F.C. et al. "ESTviewer: a Web interface for visualizing mouse, rat, cattle, pig, and chicken conserved ESTs in human genes and
human alternatively spliced variants," Bioinformatics, Vol. 21, No.10, pp.2510-2513, 2005. |
| GEMDOCK |
Yang J.M. et al. "GEMDOCK: A generic evolutionary method for molecular docking", Proteins: Structure, Function and Bioinformatics,
vol. 55, pp. 288-304, 2004. |
| GenePredict |
Web-based gene prediction service |
| GPRM |
Hu Y.J. et al.?GPRM: A genetic programming approach to finding common RNA secondary structure elements. Nucleic Acids Res. 2003 Jul
1;31(13):3446-9. |
| Hubba-Hubba |
Lin C.Y. et al.?Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology.?Nucleic Acids Res. 2008 Jul
1;36(Web Server issue):W438-43. Epub 2008 |
| KinasePhos |
Huang H.D. et al.?KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res. 2005 Jul 1;33(Web
Server issue):W226-9. |
| KPST |
KEGG Pathway Search Tool |
| MuSiC |
Multiple Sequence Alignment with Constraints |
| PDA |
Chen S.H. et al. Primer Design Assistant (PDA): A web-based primer design tool. Nucleic Acids Res. 2003 Jul 1;31(13):3751-4. |
| pKNOT |
Lai Y.L. et al.?pKNOT: the protein KNOT web server. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W420-4. Epub 2007 |
| POWER |
Lin C.Y. et al.?POWER: PhylOgenetic WEb Repeater--an integrated and user-optimized framework for biomolecular phylogenetic analysis. Nucleic
Acids Res. 2005 Jul 1;33(Web Server issue):W553-6. |
| (PS)2 |
Chen C.C. et al.?(PS)2: protein structure prediction server. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W152-7. |
| PredictProtein |
Sequence analysis and structure prediction (mirror at NTHU) |
| PSEP System |
Chuang T.J. et al.?"A Comparative Method for Identification of Gene Structures and Alternatively Spliced Variants," Bioinformatics,
Vol. 20, No. 17, pp.3064-3079, 2004. |
| RegRNA |
Huang H.Y. et al.?RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res. 2006 Jul 1;34(Web
Server issue):W429-34. |
| RepeatMasker |
Screening for low complexity DNA sequences and interspersed repeats (mirror at NCKU) |
| RMA |
Reniforced Merging Algorithms |
| RNAMST |
Chang T.H. et al. RNAMST: efficient and flexible approach for identifying RNA structural homologs. Nucleic Acids Res. 2006 Jul 1;34(Web Server
issue):W423-8. |
| SARST |
Lo W.C. et al. Protein structural similarity search by Ramachandran codes. BMC Bioinformatics. 2007 Aug 23;8:307. |
| SDSE |
Sequence Derived Structure Entropy |
| SpliceInfo |
Huang H.D. et al.?SpliceInfo: an information repository for mRNA alternative splicing in human genome. Nucleic Acids Res. 2005 Jan
1;33(Database issue):D80-5. |
| SpliceMotif |
Identify conserved sequence elements associated to mRNA splicing |
| StEQ |
Structural Entropy Query |
| Tm Predictor |
Melting Temperature Prediction : Predict thermal stability of proteins |
| UPS |
Chen S.H. et al.?The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays. BMC Bioinformatics.
2008;9 Suppl 1:S8. |
