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Unit 5 : Structural proteomics and pharmaceutical application

This component project will focus on the bioinformatics infrastructure of post-genomic analysis, especially in the field of structural proteomics and pharmaceutical application. However, other general computational tools, algorithms and educational resources will be developed as well.

A.On-line services and software
(1) Next generation sequencing related tools

(a) DSAP- Deep Sequencing Small RNA Analysis Pipeline, a web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA.

(b) SoRT2 - A Tool for Sorting Genomes and Reconstructing Phylogenetic Trees by Reversals, Generalized Transpositions and Translocations

(c) SPRING- Sorting Permutation by Reversals and block-INterchanGes

(d) ROBIN- A Tool for Genome Rearrangement of Block-Interchanges

(e) SORTBI- Sorting by Block-Interchanges

(f) 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.

(2) Structural analysis tools

(a) iSARST- Integrated service of SARST (Structure Alignment by Ramachandran Search Tool) and CPSARST (Circular Permutation Search Aided by Ramachandran Sequential Transformation)

(b) Tm Predictor- Melting Temperature Prediction; Predict thermal stability of proteins

(3) Structural database:

(a) CPDB- Circular Permutation Database. The CPDB provides resources for studying CP and CP relationships among protein structures.

(b) nsLTPDB - the non-specific Lipid Transfer Protein Database for Plant

(4) Sequence Analysis:

(a) BLAST- BLAST against PDB protein databank

(b) RPS-BLAST- Search protein or DNA sequence against Motif/Domain database

(c) FASTA- Pair-wise Sequences Alignment

(d) Gene Predict- Gene Prediction Program for Prokaryotic Genome Sequence

(5) Miscellaneous tools:

(a) KPST - KEGG Pathway Search Tool

(b) RMA- A Reniforced Merging Algorithm to searching unique peptide motifs

B.Customized data analysis on structural proteomics and pharmaceutical application