Structural Classification of Proteins (Origin Site).
1.75b release (June 2009). 38221 PDB Entries. 1 Literature Reference. 110800 Domains. (excluding nucleic acids and theoretical models).

The Predict Protein server in NTHU.
PredictProtein is a service for sequence analysis, and structure prediction. You submit any protein sequence. PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure.

BLAST against PDB protein databank in NTHU.
Choose program to use and database to search...

Search sequence against databases of profiles in NTHU.
Search your protein or DNA sequence against Motif/Domain database ...

Pair-wise Sequences Alignment (FASTA) in NTHU.

Melting temperature (Tm) database in NTHU.
Melting Temperature Prediction. Tutorial
預測當ㄧ半的雙股 DNA 解離開來時的溫度

Gene predict service in NTHU.

CustalW web interface in NTHU

DSAP- DSAP is a web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA. The functions of DSAP suite include adaptor removal, clustering of tags, classification of non-coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase databases respectively. DSAP also provide comparative miRNA expression profile analysis for up to 5 datasets. These functions all together can provide a global and comprehensive view on the expression profiles of miRNAs with sequence homology to known miRNAs in any organisms even without an available reference genome. Furthermore, DSAP's processing rate is extremely fast, it takes only 15 minutes to finish a single job of two million sequence tags. The linksis: http://dsap.life.nthu.edu.tw/

GPDB: Genome Profile DataBase.
GPDB has been developed to provide and compare features of the fully sequenced organisms in a graphic and easy-reading way. We focus on these prokaryotes including bacteria and archaea. In this post-genome era, we try to grab the information derived from both nucleotide and protein sequence in a genome-wide scale. We provide some "Genome Profile", develop on-line graphic browsing interface and use hierarchical clustering method to compare and view the difference between these organisms.
基因體分析比較工具與資料庫

WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.

RMA: Reniforced Merging Algorithms
This step-by-step RMA guide covers the basic strategy for searching unique peptide motifs by RMA system, describes the format and significance of the searched output and discusses the use of RMA tools to extract and distinguish different levels of uniqueness of unique peptide motifs.
Reference:
Chang H.T., Pai T.W., Fan T.C., Su B.H., Wu P.C., Tang C.Y., Chang C.T., Liu S.H. and Chang M.D.T. (2006) A Reinforced Merging methodology for mapping unique peptide motifs in members of protein families. BMC Bioinformatics 7:38

Currently 10 threads are running on this PC-cluster. A typical search along with superimposing 100 structures takes only 3~5 seconds. Circular permutants can be identified, even when the sequence identity is <10%. Please enjoy the speed, accuracy and convenience brought about by iSARST!

iSARST- iSARST 在多工而平行化的作業環境下整合了數種結構比對工具及兩個高效率的搜尋方法：適合尋找一般類似物的 SARST 及專門搜尋環形序列重組類似物的 CPSARST。iSARST 允許使用者一次輸入多筆蛋白質結構。資料輸入後，伺服器會先以 SARST/ CPSARST 搜尋結構資料庫，再用高準確率的結構比對軟體重新計算所得蛋白質與查詢蛋白質間的結構相似度並按相似度大小列出清單，以求快速回報資料並確保所得資訊的高準確度。 iSARST 提供互動式結構檢視介面以利使用者做進一步分析、研究。預期該伺服器可為後基因體時代的結構生物學家們提供方便的工作平台。網址為： http://sarst.life.nthu.edu.tw/iSARST/

Circular Permutation Search Aided by Ramachandran Sequential Transformation
The CPDB provides resources for studying CP and CP relationships among protein structures. This site also offers viable CP site predictions in order to facilitate the application of CP in academic researches and biotechnological developments.
高效能蛋白質環形序列重組搜尋比對工具

the Circular Permutation database
蛋白質的環形序列資料庫

KEGG pathway search tool / Tutorial