Bioinformatics

Bioinformatics or computational biology is the use of techniques from applied mathematics, informatics, statistics, and computer science to solve biological problems.

Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modelling of evolution. The terms bioinformatics and computational biology are often used interchangeably, although the latter typically focuses on algorithm development and specific computational methods. (In the biology-mathematics-computer science triad, bioinformatics will intimately involve all three components while computational biology will focus on biology and mathematics.) A common thread in projects in bioinformatics and computational biology is the use of mathematical tools to extract useful information from noisy data produced by high-throughput biological techniques. (The field of data mining overlaps with computational biology in this regard.) Representative problems in computational biology include the assembly of high-quality DNA sequences from fragmentary "shotgun" DNA sequencing, and the prediction of gene regulation with data from mRNA microarrays or mass spectrometry.

Research

Most of the scientific research I have done since May of 2000 could be described as bioinformatics or computational biology. For more information on this research, please see the following:

• Research I have done in the field

Projects / Servers

Below are links to external websites where I was the primary researcher. These are mainly Servers that I have setup:

• FastContact Server: a free energy scoring tool for protein-protein complex structures.

Version 1.0: Programmer, Server architect, and administrator; July 2005–December 2006.

Version 2.0: Programmer, Server architect, and administrator; January 2007–present.

• CBS Fungal Database: DNA structural atlases for complete chromosomes and genomes.

Programmer, Server architect, and administrator; November 2005-December 2005.

• SmoothDock Server (currently under development):

Programmer, Server architect, and administrator; January 2005–present (note: This server uses code optimised and run in parallel on 256 processors).

• LooseLoops Server (currently under development and construction):

Programmer, Server architect, and administrator; November 2004–present.

• DomainSplit Server: predicts the number of domains in a given protein (PDB format)

Server architect and administrator; September 2004–present.

• ZHunt Online Server:

Programmer; May 2000-September 2004 (note: front end by Sandor Maurice; back end by Sandor Maurice and P. Christoph Champ.)

Bioinformatics in protein analysis

[Bioinformatics in protein analysis]: The chapter gives an overview of bioinformatic techniques of importance in protein analysis. These include database searches, sequence comparisons and structural predictions. Links to useful World Wide Web (WWW) pages are given in relation to each topic. Databases with biological information are reviewed with emphasis on databases for nucleotide sequences (EMBL, GenBank, DDBJ), genomes, amino acid sequences (Swissprot, PIR, TrEMBL, GenePept), and three-dimensional structures (PDB). Integrated user interfaces for databases (SRS and Entrez) are described. An introduction to databases of sequence patterns and protein families is also given (Prosite, Pfam, Blocks). Furthermore, the chapter describes the widespread methods for sequence comparisons, FASTA and BLAST, and the corresponding WWW services. The techniques involving multiple sequence alignments are also reviewed: alignment creation with the Clustal programs, phylogenetic tree calculation with the Clustal or Phylip packages and tree display using Drawtree, njplot or phylo_win. Finally, the chapter also treats the issue of structural prediction. Different methods for secondary structure predictions are described (Chou-Fasman, Garnier-Osguthorpe-Robson, Predator, PHD). Techniques for predicting membrane proteins, antigenic sites and postranslational modifications are also reviewed.

See also

• Genome Sequencing and Databases: Genome Sequencing, Phred, Phrap, Consed, Sequin
• Database Searching for Similar Sequences: FASTA, BLAST, SSEARCH, Dotter, Align, Clustal, Meme, Fasta, Ssearch, Blast
• Phylogenetic Prediction: CN3D, MMDB, VAST, PREDATOR, Phylip
• Gene Analysis: HMMER, MAST, PSI-BLAST - Sim4, Genscan, GrailExp