Protocols, Bioinfomatic Tools, and Useful Web links

Soares Lab Protocols

Outside Links

• Commonly Used Links
• DDBJ    Japanese national repository nucleotide sequence database


• EBI    European centre for research and services in bioinformatics


• Ensembl    A software system which produces and maintains automatic annotation on selected eukaryotic genomes.


• ExPASy    Site that contains utilities for analysis of protein sequences and structures


• MEME    Using MEME/MAST one can discover motifs in groups of related DNA or protein sequences and also search sequence databases using motifs


• NCBI    US national repository that contains computational, genomic, and biomedical databases. It also stores several software utilities to help with this information


• RGD    Collects and integrates data generated from rat genetic and genomic research efforts


• SSR    Organization promoting the study of human and animal reproduction


• TIGR    collection of curated databases containing DNA and protein sequence, gene expression, cellular role, protein family, and taxonomic data for microbes, plants and humans


• UCSC    Contains reference sequences and working draft assemblies for a large collection of genomes. It also houses several utilities (Blat, Genome Browser, VisiGene...) to explore those sequences
• Gene Expression Links
• BodyMap    A data bank of expression information of human mouse genes in various tissues and cell types


• ExpressDB    Relational Database containing yeast and E. coli RNA expression data.


• HuGEIndex    Provides a comprehensive database to aid in understanding the expression of human genes in normal human tissues


• SMD    Database containing microarray data generated by Stanford researchers and their collaborators
• Gene Prediction Links
• GeneMark    A family of gene prediction programs


• GENSCAN    Used for predicting the locations and exon-intron structures of genes in genomic sequences


• GFF    A protocol for formatting genomic sequence data


• Glimmer    System for finding genes in microbial DNA


• tRNAscan-SE    Used to search for tRNAs in a genomic sequence
• Gene Regulation Links
• Cister    Predicts regulatory regions in DNA sequences by searching for clusters of cis-elements


• DBTSS    Database of human transcriptional start sites


• DCPD    Contains a list of Drosophila melanogaster core promoters aligned by their empirically determined transcription start site


• DPInteract    Protein binding sites on E. coli DNA


• EPD    Annotated non-redundant collection of eukaryotic POL II promoters


• SCPD    Explore the promoter regions of ~6000 genes and ORFs in yeast genome
• Genome-Scale Analysis
• COGs    Grouping of protein sequences encoded in complete genomes


• GENECENSUS    Various whole genome comparisons


• MBGD    Database used for comparative analysis of completely sequenced microbial genomes


• STRING    A database of known and predicted protein-protein interactions
• Downloadable Utility Links
• ImageJ    Image processing and analysis in Java


• Protein Explorer    A RasMol-derivative for looking at macromolecular structure and its relation to function


• MolviZ    Contains several downloadable tools that deal with molecular visualization
• Metabolic, Gene Regulatory, and Signal Transduction Links
• aMAZE    Database for the representation of information on networks of cellular processes: genetic regulation, biochemical pathways, signal transductions


• DIP    Catalogs experimentally determined interactions between proteins


• KEGG    Site devoted to Computational prediction of higher-level complexity of cellular processes and organism behaviors from genomic and molecular information


• SPAD    Integrated database for the genetic information and signal transduction systems


• thesignalinggateway    Collaboration between academia and scientific publishing and is designed to facilitate navigation of the complex world of research into cellular signaling
• Motif and Pattern Finding Links
• AlignACE    A program which finds sequence elements conserved in a set of DNA sequences


• Gibbs Motif Sampler    Identify motifs in DNA or protein sequences


• Pratt    Used to discover patterns conserved in sets of unaligned protein sequences


• SAM    Tools for creating and using Hidden Markov Models
• Online Utility Links
• CBS Prediction Services     Prediction of protein subcellular localization and various sites in protein and nucleotide sequences


• ESTparser     Visualization of alternate mRNA 3'-ends through EST alignment


• ExPASy Links    A lot of different links


• MELTING    Computes the enthalpie, the entropy, and the melting temperature for the binding to its complementary template, of an oligonucleotide


• mRNA Extension Using Genomic EST Alignments    Extends missing ends of an mRNA using EST and genome sequence data


• pI/Mw Tool    Calculates the theoretical pI(isoelectric point) and Mw(molecular weight) for a list of sequences


• PSORT    Program used fro the prediction of protein localization sites in cells


• Primer3    Utility for designing primers


• SDSC Biology Workbench    Tool that allows searching of many popular protein and nucleic acid sequence databases


• Vienna RNA Package    RNA secondary structure prediction and comparison utility
• Other Useful Links
• Biology of the Mammary Gland    Program to integrate various aspects of mammary gland biology


• CGAP    Resources used for the study of gene expression profiles in normal, precancer, and cancer cells.


• Cytochrome P450    Database of cytochrome P450 sequences


• EMBnet    Contains databases and utilities for research in the biosciences


• The Endocrine Society    Professional organization for the study of endocrinology


• ENZYME    Repository of information relative to the nomenclature of enzymes


• Feature Table    Standard format for annotating nucleic acid sequences


• GDB    World-wide database for the annotation of the human genome


• Gene Ontology    Provides a controlled vocabulary to describe gene and gene product attributes in any organism


• GENIE    Gene finder based on generalized hidden markov models


• Genotator    Annotation workbench that runs various sequence analysis programs


• GRAILEXP    A suite of tools used to locate protein coding genes, EST/mRNA alignments, certain types of promoters, polydenylation sites, CpG islands, and repetitive elements


• HGVbase    Provides an accurate, high utility, and ultimately fully comprehensive catalog of normal human gene and genome variation,


• HGNC    Concerned with making sure that each human gene has an appropriate name and symbol(short-form abbreviation)


• Human Genome Resources    Provides genomic information for Homo sapiens


• MethDB    Provides a database that stores DNA methylation data


• REBASE    A collection of information about restriction enzymes and related proteins


• MGC    Provides full-length open reading frame clones for human, mouse, rat, and bovine genes


• Pfam    Large collection of multiple sequence alignments and hidden Markov models convering many common protein families


• SCOP    Provides structural and evolutionary relationships between proteins with known structures


• SMART    Allows for the identification and annotation of genetically mobile domains and the analysis of domain architectures


• SNP    Provides data that has been collected about single nucleotide polymorphisms in the human genome
• Phylogeny and Taxonomy Links
• PHYLIP    A package of programs for inferring phylogenies


• Species 2000    Enumerating all known species of organisms on Earth as the baseline dataset for studies of global biodiversity


• TreeBase    A relational database containing phylogenetic information


• Tree of Life    Provides identification keys, figures, phylogenetic trees, and other systematic information for a group of organisms


• TreeView    A program that allows for viewing of the contents of NEXUS, PHYLIP, Henning86, Clustal, or other format tree file
• Protein Links
• PIR    Provides a centralized source for protein sequences and functional information


• Swiss-Prot    A protein sequence database which provides a high level of annotation including description of the function of a protein, its domains structure, post-translational modifications, variants, and such
• Protein Domain Search Tool Links
• InterPro    Database of protein families, domains, and functional sites in which identifiable features can be applied to unknown protein sequences


• PRINTS    A database of protein motif fingerprints


• ProDom    A set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases


• PIMA Profile Search    Allows searching of protein functional diagnostic profiles


• TIGRFAMs    Protein families based on Hidden Markov Models
• Structural Protein Links
• BioInfoBank MetaServer    Provides a gateway to protein structure and function prediction methods


• CATH    A classification of protein domain structures, which clusters proteins at four major levels Class Architecture, Topology, and Homologous Superfamily


• DSSP    Defines the secondary structure, geometrical features, and solvent exposure of proteins given atomic coordinates in Protein Data Bank format


• HSSP    Database containing homology derived secondary structures of many proteins


• K2    Protein structure alignment program


• PDB    Provides a variety of tools and resources for studying the structures of proteins


• PredictProtein Server    After submitting a protein structure the program retrieves similar sequences in the database and predicts aspects of protein structure


• PSIPRED    Allows one to submit a protein sequence and then the program performs a prediction of your choice and gives you the results


• SWISS-MODEL    A protein structure homology modeling server
• Sequence Links
• BOXSHADE    A program for creating pretty output of multiple aligned protein/DNA data


• ClustalW    A general purpose multiple sequence alignment program for DNA or proteins


• PipMaker    Computes alignments of similar regions in two DNA sequences


• Spidey    A mRNA-to-genomic alignment program


• T-COFFEE    Multiple sequence alignment package


• USC Sequence Alignment Server    Performs Smith-Waterman and other dynamic programming sequence alignment algorithms


• VISTA    Comprehensive suite of programs and databases for comparative analysis of genomic sequences


• Wise2    Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors
• Transmembrane Helix Prediction Links
• SOSUI    Classification and secondary structure prediction system for membrane proteins


• TMHMM    Prediction of transmembrane helices in proteins


• TMpred    A program that makes a prediction of membrane-spanning regions and their orientation
• Various Other Organism Database Links
• BDG    Maintains the biological annotations of the Drosophila melanogaster sequence


• dictyBasse    Collection of Dictyostelium genome information


• ecogene    Contains updated infromation about E. coli K-12 genome and proteome sequences, including extensive gene bibliographies


• FlyBase    Contains genetic and molecular data for Drosophila


• GOLD    Provides comprehensive access to information regarding complete and ongoing genome projects around the world


• HIV Database    Contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials


• MGI    Provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse


• SGD    A scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae


• tair    Collects and maintains a database of the genetic and biology data for Arabidopsis thaliana


• TIGR-CMR    Displays information on all of the publicly available, complete prokaryotic genomes


• WormBase    Dedicated to providing accurate, current, accessible information concerning the genetics, genomics, and biology of C. elegans and some related nematodes


• ZFIN    Database of many types of information for zebrafish researchers