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
(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
(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|