Biological Sequence AnalysisBiological sequence analaysis refers to the extraction and use of information derived from the sequence of biological macromolecules: DNA (deoxyribonucleic acid), RNA (ribonucleic acid), and proteins are macromolecules which are unbranched polymers built up from smaller units. In the case of DNA these units are the 4 nucleotide residues A (adenine), C (cytosine), G (guanine) and T (thymine) while for RNA the units are the 4 nucleotide residues A, C, G and U (uracil). For proteins the units are the 20 amino acid residues:
Analysis of sequences of DNA, RNA or proteins can reveal a lot of information about their function. Some common analyses include: determination of the functional units (genes) from the raw sequence of a completely sequenced genome, prediction of the three dimensional structure and function of a protein from its primary structure. Our current research in biological sequence analysis has two broad thrusts: the development of general purpose tools, and the development of tools specially tailored to the needs of collaborators in WEHI and elsewhere. Examples of the former include the gene prediction program Phat and the coiled-coil prediction program Marcoil , while we have yet to publish any examples of the latter. A wide range of mathematical, statistical and computational problems arise in our work in the area of biological sequence analysis. We make extensive routine use of publicly available tools for standard problems, and to help meet the needs of more specific multi-step problems. These tools include Blast, FASTA and Clustal W fast local and careful multiple alignment, MEME/MAST for motif identification, Genscan and GeneId for single species gene prediction in human and mouse, SLAM and Twinscan for joint human-mouse gene prediction, and a host of tools for the prediction of transmembrane domains, promotors, and other special motifs/domains/signals. Selected Recent Publications
SoftwarePhatPhat is a program for finding genes in eukaryotic organisms. Marcoil MARCOIL is a hidden MARkov model-based program that predicts existence and location of potential coiled-coil domains in protein sequences. Genenest GeneNest provides a visualization of gene indices of Human, Mouse, Arabidopsis, Zebrafish and Drosophila. MEME/MAST Discover motifs (highly conserved regions) in groups of related DNA or protein sequences using MEME and, search sequence databases using motifs using MAST. TWINSCAN TWINSCAN is a modern gene prediction system designed to analyze eukaryotic genomic sequences. SLAM SLAM is a comparative-based annotation and alignment tool for syntenic genomic sequences that performs gene finding and alignment simultaneously and predicts in both sequences symmetrically. GENSCAN Genscan predicts the locations and exon-intron structures of genes in genomic sequences from a variety of organisms. GENEID GENEID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. BLAT BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more. Protein BLAT works in a similar manner. TMpred The TMpred program makes a prediction of membrane-spanning regions and their orientation. MEROPS The MEROPS database provides a catalogue and structure-based classification of proteases, together with additional information about them. Comments/Questions? Contact bioinf@wehi.edu.au. |