Links
Ozcelik Links
University of Toronto
Genetic Links
Bioinformatics Links
DNA - SNPs
| ALFRED | The Allele Frequency Database from Kidd Lab at Yale University School of Medicine. |
| BLAST Gene Transcript | Translates a specified SNP onto a GenBank sequence and then determines whether or not it results in an amino acid substitution. |
| CGAP | Genetic variation in genes important in cancer (Genetic Annotation Initative at the National Cancer Institute). |
| dbSNP | A database of SNPs and short deletion and insertion polymorphisms at NCBI. |
| HGVbase | A fully comprehensive, non-redundant and highly curated and annotated catalog of normal human gene and genome variation. |
| Human SNP Database | SNPs discovered by Whitehead Institute/MIT Center for Genome Research. |
| GeneSNP | Environmental Genome Project web resource which integrates gene, sequence and polymorphism data into individually annotated gene models. |
| PolyPhen | Predicts possible impact of an amino acid substitution on the structure and function of a human proteins. |
| SIFT | Predicts the amino acid substitutions affect on protein function. |
| SNP500 | Part of the Cancer Genome Anatomy Project specifically designed to generate resources for the identification and characterization of genetic variation in genes important in cancer. Provides a central resource for sequence verification of SNPs. |
| SNPper | CHIP Bioinformatics Tools |
| The SNP Consortium | The Consortium is aiming to give information about up to 300 000 SNPs to the public. |
DNA - Repeats
| CHLC | Maps CHLC Integrated Map Data Sets (Search for markers). |
| Draft of Human Genome | Tandem Repeats Links, Info., and Programs, Draft of Human Genome. |
| GIRINST | Repeats info in Prokaryotes and Eukaryotes (registration required). |
| GRID | Genome Repeats Information Database. |
| GPMS | Genomes, Polymorphism and Minisatellites Minisatellites Database (Prokaryotes and some Eukaryotes). |
| MRD | Consists of 5 tables which provide summary and detailed views of microsatellites, the genomic regions they belong to and their associations with genes and STS. Tables for Repeats associated with genes. |
| PTRF | Versions of Perfect Tandem Repeat Finding Executables (Unix and Mac /OS). |
| Recon | A package for automated de novo identification of repeat families from genomic sequence. |
| Repeat Masker | Screens DNA sequences for interspersed repeats and low complexity DNA sequences. |
| REPRO | The program is able to recognize distant repeats in a single query sequence (online). |
| REPuter | The program family provides state of the art software solutions to compute and visualize repeats in whole genomes or chromosomes (long seq, whole genome). Stand alone (UNIX), online (limited). |
| SLAM | Gene finding and alignment simultaneously. Comprehensive list of all Human genes by Chr. location. Useful site for finding repeats within or close to genes . |
| STR DB | These data are intended to benefit research and application of short tandem repeat DNA markers to human identity testing. (forensic). |
| SSRD | Simple Sequence Repeat Database for the human genome. |
| SSRDB | A database of simple sequence repeats (SSRs) in eukaryotes. Human Chromosome 22 and other species, (Supplementary material to the paper). |
| TRDB | Very useful linkTables of genes containing Trinucleotide repeats. |
| TRH | Tandem Repeats History Reconstruction. |
| TRF | Tandem Repeat Finder 3.21. Available for download in all platforms. |
RNA
| ARED | Human AU-Rich Element-Containg mRNA Database. |
| RNase P | Compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information. |
| RNAmods | A comprehensive listing of post-transcriptionally modified nucleosides from RNA. |
| Small RNA database | Small RNA database. |
| UTR DB | Database collection of 5’ and 3’ UTR sequences of eukaryotic mRNA. Can be downloaded from the ftp site. |
Protein Interactions
| BIND | Contains interaction, molecular complex and pathway records. Interaction information comes from the literature, submitters and other databases. |
| PID | Combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data is curated, both, manually by expert curators and also automatically using computational approaches. |
| BioGRID | Database of genetic and physical interactions that contains interaction data from many sources, including several genome/proteome-wide studies, the MIPS database, and BIND. |
| MINT | Designed to store functional interactions between biological molecules (proteins, RNA, DNA). Beyond cataloguing the formation of binary complexes, it also stores other type of functional interactions namely enzymatic modifications of one of the partners. Presently MINT focuses on experimentally verified protein-protein interactions. |
| STRING | Predicts functional associations among genes/proteins. |
Protein Structure
| CATH | Hierarchical classification of protein domain structures. |
| PDBeFold | Network service for comparing protein structures in 3D. |
| JPred | A consensus secondary structure prediction server. |
| PDB | Single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. |
| Protein Motion | Database of macromolecular movements including motions of loops, domains, and subunits. |
| SCOP | Structural classification of proteins database. |
| SWISS MODEL | An autumated comparative protein modelling server of Swiss Institute of Bioinformatics. |
| VAST | NCBI based. Compares directly related structures. |
Protein Signature Sequence
| CDD | NCBI Conserved Domain Search. |
| CDART | NCBI Conserved Domain Architecture Retrieval Tool. |
| InterPro | Database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. |
| Pfam | A large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. |
| Motif Scan | Motif Scan in Protein Sequences. |
| PRINTS | A compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. |
| ProScale | Computes and represents the profile produced by any amino acid scale on a selected protein. |
| Swiss-Prot | Highly curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. |
| IBM CBC | IBM Bioinformatics Group. Sequence Pattern Discovery. |
Protein Stability
| PDB | Single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. |
Diagnostics
| Breast Cancer Information Core (BIC) | An Open Access On-Line Breast Cancer Mutation Database. |
Bioinformatics Tools
| PLINK | A free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. |
| Haploview | Designed to analyze and visualize patterns of linkage disequilibrium(LD) in genetic data. Haploview can also perform association studies, choosing tagSNPs and estimating haplotype frequencies. |
Bioinformatics - Bibliographic Databases
| NAL | Bibliographic database of citations to the agricultural literature. |
| PubMed | Biomedical literature. |
| SeqAnalRef | Bibliographic reference data bank relative to papers dealing with sequence analysis. Stores the references of articles from the expanding field of mathematical and computer analysis of biomolecular sequences. |
Bioinformatics - Homology
| BLAST | Designed for speed, with a minimal sacrifice of sensitivity to distant sequence relationships. Applies a heuristic algorithm that seeks local as opposed to global alignments and is therefore able to detect relationships among sequences that share only isolated regions of similarity. |
| ClustalW | Translates a specified SNP onto a GenBank sequence and then determines whether or not it results in an amino acid substitution. |
| DCA | Divide-and-Conquer Multiple Sequence Alignment. |
| DIALIGN | Constructs pairwise and multiple alignments by comparing whole segments of the sequences. |
| FASTA | Can be very specific when identifying long regions of low similarity especially for highly diverged sequences. |
Bioinformatics - Molecular Evolution
| MEGA | Molecular evolutionary genetics analysis. |
| PHYLIP | A package of programs for evolutionary genetics and phylogenetic analysis. |
| SIFT | Predicts the amino acid substitutions affect on protein function. |
| Tree Of Life | Phylogeny and biodiversity database containing information about the diversity of organisms on Earth, their history, and characteristics. The information is linked together in the form of the evolutionary tree that connects all organisms to each other. |
| TreeView | Program for displaying phylogeny trees. |
Bioinformatics - Organismal Databases
| FlyBase | Drosophila Database. |
| GeneCards | Database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others. |
| HUM-MOLGEN | International Communication forum in human molecular genetics. |
| MGI | Mouse Genome Database. |
| OMIA | Online Mendelian Inheritance in Animals. |
| OMIM | Online Mendelian Inheritance in Man. |
| SGD | Saccharomyces Genome Database. |
| TAIR | Arabidopsis thaliana Database. |
| WormBase | Caenorhabditis elegans. |
Bioinformatics - Molecular Biology Databases
| BioCarta | Charting Pathways of Life. |
| CEDAR | Human Genetics Division, School of Medicine , University of Southampton . Web site, link to several marker sets and SNPs related to general cognitive ability. |
| CMG | The Center for Medical Genetics at Masrshfield. |
| COGs | Phylogenetic classification of proteins encoded in complete genomes. |
| DDBJ | DNA Data Bank of Japan. |
| EMBL | European Molecular Biology Lab. |
| NAR Database Issue | Baxevanis Molecular Biology Database Collection. |
| NCBI | National Centre for Biotechnology. |
| PDB | Protein Data Bank. |
| PIR | Protein Information Resource. |
| Pseudo | Pseudogenes and Intergenic Analyses. |
| Swiss-Prot and TrEMBL | Curated protein sequence database. |
| UCSC Genome | UCSC genome main web site. |
Bioinformatics - Mutation Databases
| Androgen Receptor | Androgen Receptor Gene Mutations Database. |
| BTKbase | Mutation registry for X-linked agammaglobulinemia. |
| CYBAbase | Mutation registry for autosomal recessive chronic granulomatous disease (CGD), deficiency of p22phox. |
| CYBBbase | Mutation registry for X-linked chronic granulomatous disease (previously known as X-CGDbase). |
| Fanconi Anemia | Fanconi Anemia Mutation Database. |
| MUTATION DATABASES | Mutation Databases. |
| Werner Syndrome | Werner Syndrome Mutational Database. |
Bioinformatics - Sequence Analysis Tools
| Biology WorkBench | Search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems. |
| COILS | Compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. |
| Compute PI | Allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of Swiss-Prot and/or TrEMBL entries or for a user entered sequence. |
| EMBOSS | Detection of regions of genomic sequences that are rich in the CpG pattern. |
| DCA | Divide-and-Conquer Multiple Sequence Alignment. |
| DIALIGN | Constructs pairwise and multiple alignments by comparing whole segments of the sequences. |
| ORF Finder | Finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database. |
| SignalP | Predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. |
| TMPRED | Predicts membrane-spanning regions and their orientation. |
| Translate | Allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence. |
| VecScreen | Identifies segments of a nucleic acid sequence that may be of vector origin. |
Computer - Flash
| Developing Webs | Total Guidance for building and maintaing a website and more. |
| Flash Button Generator | Flash Button Generator. |
| Flash Kit | Flash Tutorials & Resources. |
| Macromedia Flash | Macromedia Flash Samples & Tutorials. |
Computer - HTML
| Color Codes | Color Chart for Web Development. |
| Developing Webs | Total Guidance for building and maintaing a website and more. |
| HTML Tutorial | HTML Tutorial. |
Computer - Java
| Java API | JavaTM 2 Platform, Standard Edition, v 1.3.1 API Specification. |
| Java Sun.Com | Java Sun.Com, the Source for Java Technology. |
| Java Developer Tutorials and Training | Java Developer Tutorials and Training. |
| Java Programming Resources | Java Programming Resources. |
Computer - Perl
| CPAN | Comprehensive Perl Archive Network with open source Perl modules. |
| perl.org | The Source for Perl. |
| Perl Basics | Perl Basic Functions. |
Computer - Photoshop
| Developing Webs | Total Guidance for building and maintaing a website and more. |
| Phong PhotoShop Tutorial | PhotoShop Tutorials. |
Computer - Software
| Download.com | Download.com. |
| Macromedia Downloads | Macromedia Downloads. |
| Tucows | Free Tucows Downloads. |
