Analysis Tools



12/29/2005 Update

Jong @ PC Lyu's Lab

Life Science, NTHU


This is a former mirror of the BNL PDB in NTHU.

Structural Classification of Proteins (Origin Site). 1.69 release (July 2005). 25973 PDB Entries. 1 Literature Reference. 70859 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.
Data and Tool Integration.
Java interface for EMBOSS
EMBOSS (European Molecular Biology Open Software Suite) is a suite of free software tools for sequence analysis. There are a wide variety of programs that make up the suite, ranging in application from database searching to presentation of sequence data.

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.
Gene predict service in NTHU.
CustalW web interface in NTHU
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.
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.
Structure Alignment with Ramachandran Search Tool
Searching similar protein structures of the specified protein in PDB (Total 67,411 chains of 31,059 proteins in PDB of 2005/5/24)
KEGG pathway search tool
What's New
Jan 13, 2006


Happy New Year


Bioinformatics Core
:: Program for Promoting Academic Excellence of Universities (PhaseⅡ) :: Project Period: April 1, 2005-March 31, 2009