Biology

RestrictionMapper RestrictionMapper- Finds restriction enzyme cleavage sites in linear and circular DNA sequences. Provides also a virtual digest function. WatCut WatCut- Provides restriction analysis, silent mutation scanning and SNP-RFLP analysis. Allows for utilization of all commercially available type II restriction enzymes. REBASE REBASE- The restriction enzyme database. Maintained by the New England Biolabs, USA. Sequence Alignment and Modeling System Sequence Alignment and Modeling System- Implementation of hidden Markov models for sequence analysis. Free UNIX software for nonprofit groups, and sequences can be submitted onlin… The ISREC Group Servers The ISREC Group Servers- Detection and assessment of similarity between distantly related sequences by means of a variety of remotely-executable software - from the Swiss Inst. fo… BLAST BLAST- Suite of alignment tools to detect conserved sequences, similar domain architecture, gene expression profiles, and SNP using protein or nucleotide targets. Includes support… ESPript ESPript- Formatting of multiple sequence alignments to a color postscript file. Can include graphical features by using PDB entry. GENESTREAM Bioinformatics Resource Server GENESTREAM Bioinformatics Resource Server- Sequence comparision and search programs, including the rigorous Smith-Waterman algorithm (in FastA and Ssearch) - from the IGH, Montpel… mreps : maximal tandem repeats search mreps : maximal tandem repeats search- Open source tool for identifying serial repeats (tandem repeats) in DNA sequences. WU-BLAST Archives WU-BLAST Archives- Sensitive, selective, and rapid sequence database searching with gapped alignments - from Washington Univ.-St.Louis. Annmap Genome Browser Annmap Genome Browser- An interactive genome browser supporting multiple species. It displays mapping between Affymetrix Exon Arrays and their corresponding genes and exons. Annmap Genome Browser Annmap Genome Browser- An interactive genome browser supporting multiple species. Annmap displays mapping between Affymetrix Exon Arrays and their corresponding genes and exons. Pedant Pedant- Offers analysis of protein sequence sets from individual sequences to complete genomes. PhenomicDB PhenomicDB- PhenomicDB is a multi-organism phenotype/genotype database. Users can compare the phenotypes of a gene over many organisms simultaneously. Saccharopolyspora erythraea genome Saccharopolyspora erythraea genome- Website for S. erythraea NRRL23338 genome sequencing project. MaizeGDB MaizeGDB- MaizeGDB is the community database for biological information about the crop plant Zea mays. EURExpress II EURExpress II- A transcriptome-wide atlas database for the developing mouse embryo established by RNA in situ hybridization. SOL Genomics Network SOL Genomics Network- Integrated clade oriented genome database for the Solanaceae (tomato, potato, pepper, eggplant etc.) and other Asterids. Contains genetic maps, gene sequence… Gramene: A comparative genomic resource for grains Gramene: A comparative genomic resource for grains- Gramene is a curated, open-source data resource that provides agricultural researchers and plant breeders with biological and g… Human Ageing Genomic Resources Human Ageing Genomic Resources- A collection of databases and tools designed to help researchers understand the genetics of human ageing. GenomeSeek GenomeSeek- A fully-searchable database to provide information and easy access to over 200 current and completed genome projects. Saccharomyces Genome Database Saccharomyces Genome Database- Resource for genomic information on yeast, with tutorial on gene ontology, homology searches and comparisons. Includes links to tools, related confe… Rat Genome Database Rat Genome Database- Contains rat genomic data such as genes, SSLPs, ESTs, QTLs, and strain information and tools such as vcmap, genome scanner, rhmap server, metagene. Also has a… Mouse Genome Informatics Mouse Genome Informatics- This site contains information on mouse genetic markers, mapping, phenotypes, mammalian homology and gene expression. All data are searchable through a s… FlyMine FlyMine- An integrated database of genomic, expression and protein data for Drosophila and Anopheles. QGRS Mapper QGRS Mapper- Generates information on composition and distribution of putative Quadruplex forming G-Rich Sequences (QGRS) in nucleotide sequences and NCBI genes. GenomeScan GenomeScan- Prediction of locations and exon-intron structures in genomic sequences, incorporating protein homology information when predicting genes from DNA sequence. Webserver … GenScan Server GenScan Server- Identification of gene features such as exons and splice sites in genomic DNA. Psort Psort- Portal to protein subcellular localization resources and tools, for prediction in gram negative bacteria. Maintained by the Brinkman Laboratory, Simon Fraser University, BC… Microarray Database Gateway Microarray Database Gateway- Tools for managing, accessing, and analyzing cDNA microarray data generated by the NCI Div. of Clinical Sciences µArray Center - from the BioInformati… MiCoViTo MiCoViTo- Tools for comparing, exploring and visualizing correlated genes in two microarray experiments in yeast transcriptomes. Includes visualization of induced gene groups base… Mascot Mascot- Search engine that uses mass spectrometry peptide data to identify proteins from primary sequence databases. Protein sequence analysis: A practical guide Protein sequence analysis: A practical guide- A web-based tutorial associated with "Introduction to bioinformatics" published by Addison Wesley Longman. Institute for Genomics and Bioinformatics Institute for Genomics and Bioinformatics- Specializing in making publicly available software and database services for computational biology. Bioinformatics FAQ Bioinformatics FAQ- Summary of basics of bioinformatics for the intelligent newcomer. Bioinformatics On-line Courses and Tutorials Bioinformatics On-line Courses and Tutorials- A list of on-line course materials and tutorials for bioinformatics and computational biology. Index of Computational Molecular Biology and Bioinformatics Courses Index of Computational Molecular Biology and Bioinformatics Courses- Listing of computational molecular biology course pages that have extensive online course materials. Bioinformatics and Computational Biology at ISU Bioinformatics and Computational Biology at ISU- An Interdisciplinary Graduate Program offering Ph.D. and M.S. degrees in Bioinformatics and Computational Biology (BCB) at Iowa St… Canadian Bioinformatics Workshops Canadian Bioinformatics Workshops- Offers short courses in bioinformatics, genomics and proteomics in various cities across Canada. Bitesize Bio Bitesize Bio- Online magazine and community for molecular and cell biology researchers. Provides daily tech tips and news articles on advances in molecular and cell biology. Biochemist e-volution Biochemist e-volution- Magazine of the Biochemical Society, containing features, news, events, announcements, book reviews and company information Molecular Systems Biology Molecular Systems Biology- A peer-reviewed open access journal from EMBO Press that publishes high-quality research in the fields of systems biology, synthetic biology and systems… The Journal of Biological Chemistry The Journal of Biological Chemistry- Articles in this journal deal with biological processes at the biochemical or molecular level. Fulltext accessible after 1 year every January Journal of Inorganic Biochemistry Journal of Inorganic Biochemistry- Publishes research papers and short communications in the following areas: the chemistry, structure, and function of metalloenzymes; the interac… Journal of Molecular Structure: THEOCHEM Journal of Molecular Structure: THEOCHEM- Publishes research related to the theory and modelling of molecular systems. Contents lists and abstracts starting from 2000; full text f… Process Biochemistry Process Biochemistry- Publishes articles devoted to the science and technology of the application of living organisms to the production of materials for the benefit of mankind. Matrix Biology Matrix Biology- Publishes studies utilizing most scientific technologies including molecular biology, cell biology, immunochemistry, structural biology, computational biology, the… Current Opinion in Chemical Biology Current Opinion in Chemical Biology- Advances in the field by accessing the views of experts. Includes guide to authors, links to abstracts, complimentary articles and full text a… International Journal of Biological Macromolecules International Journal of Biological Macromolecules- Research into the structure and functional properties of natural proteins, carbohydrates and nucleic acids, with modeling their… Journal of Molecular Biology Journal of Molecular Biology- Weekly publication of original scientific research, concerning studies of organisms or their components at the molecular level. Full text articles av…