 One of many library books on nucleic acid analysis |
Use Socrates to find printed or digital books or journals at Stanford. Digital Journals available to the Stanford community are listed in Electronic Journals and Newspapers. To find journal articles on Nucleic Acid Analysis, use one of the databases listed under Article Resources below. Under Web Resources, find organizations, government agencies, or web sites related to the topic. Can’t find what you need? Comments or questions? Contact Falconer Biology Library. |
Article Resources
BIOBASE Knowledge Library (BKL), combining the PROTEOME and TRANSFAC suites of databases, offers rich, high quality content and integrated analysis tools spanning gene regulation and pathways to fully annotated genomes. These database products offer a combination of computational and experimental data. PROTEOME is a comprehensive knowledge resource for the complete known proteomes of selected species, including humans. TRANSFAC compiles data on transcription factors, their experimentally-proven binding sites, and regulated genes.
Also known as BIOSIS Previews, indexes the worldwide literature of research in the biological and biomedical sciences. The database covers the entire field of life sciences including original research reports and reviews in field, laboratory, clinical, experimental, and theoretical work. BIOSIS indexes journals, technical reports, meeting proceedings, United States patents, and books in biology, biomedicine, and related areas. The database indexes literature published from 1926 to the present. Over 500,000 journal articles and other documents from over 6,000 journals and other sources are indexed each year.
Developed by the National Center for Biotechnology Information (NCBI), Pubmed is a free version of MEDLINE that offers links to GenBank records, other molecular sequence data, and other resources. MEDLINE, produced by the National Library of Medicine, is an index to journal articles in medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences, including both basic biomedical sciences and clinical practice. It indexes over 4,000 journals. The database contains citations from 1950 to the present with some older citations. An important feature of MEDLINE is the use of Medical Subject Headings (MeSH), a powerful tool for searching specific topics or for comprehensive general searches. MEDLINE is also available to Stanford users via EBSCO, ISI Web of Knowledge, NLM Gateway, OCLC ,and Ovid.
The Web of Science service, available via ISI Web of Knowledge, includes three core component databases: the expanded version of Science Citation Index (SciSearch), Social Sciences Citation Index, and Arts & Humanities Citation Index. The Science Citation Index provides access to current and retrospective bibliographic information, author abstracts, and cited references found in the world's leading scholarly science and technical journals covering over 100 disciplines from 1900 to the present. An important feature of SciSearch is the ability to perform cited reference searching to find recent articles that cite an earlier work.
xSearch, developed through the Stanford University Libraries' partnership with Deep Web Technologies, provides Stanford researchers and students with a single search option for multiple online resources. Searches may be limited to specific databases, or all available sources may be searched simultaneously. Search results are merged into one relevance ranked list, and are clustered by topic, author, source publication, publisher, and date. Custom searches using any selection of available databases can be created and re-used. Users may also create alerts in order to be informed automatically of new items that match search criteria.
Web Resources
The Arabidopsis Information Resource offers genomic information, as well as analysis tools, links and downloads all about Arabidopsis. It is also searchable for information on genes, DNA, genetic markers, proteins and polymorphisms.
ArrayExpress is a public archive for functional genomics data compliant with MIAME- and MINSEQE requirements in accordance with MGED recommendations. The Gene Expression Atlas uses a curated, re-annotated subset of data from the Archive to provide information about gene expression under various biological conditions.
The Alternative Splicing and Transcript Diversity (ASTD) database project, maintained by EMBL-EBI, is creating a database of alternative splice events and transcripts of genes from human, mouse and rat. Full length transcripts are generated with the aim of understanding the mechanism of alternative splicing on a genome-wide scale.
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
The CBS website contains an assortment of information including news, events, research groups, prediction servers, bioinformatics tools, datasets and publications. The prediction servers have information on both nucleotide and amino acid sequences.
CiteXplore combines literature searches of MEDLINE/PubMed and full-text databases such as PubMedCentral and patents with text mining tools for biology. Search results are cross referenced to EBI applications based on publication identifiers. Links to full text versions are provided where available.
This E. Coli database has information on genotypes for specific strains of E.Coli in the CGSC database. Also available are gene names, properties, linkage maps, gene product information, and mutation information.
The European Genome-phenome Archive (EGA), maintained by EMBL-EBI, is designed to be a repository for all types of genotype experiments, including case control, population, and family studies. We will include SNP and CNV genotypes from array based methods and genotyping done with re-sequencing methods. This data may be either publicly available or limited access, depending on the design of the study.
The EMBL Nucleotide Sequence Database (also known as EMBL-Bank), maintained by EMBL-EBI, is Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications. The database is produced in an international collaboration with GenBank (USA) and the DNA Database of Japan (DDBJ). Each of the three groups collects a portion of the total sequence data reported worldwide, and all new and updated database entries are exchanged between the groups on a daily basis.
EMBL-CDS is a database of nucleotide sequences of the CDS (coding sequence) features, as annotated in EMBL database. EMBL-CDS record contains the nucleotide sequence of the CDS region, accompanying annotation from the parent nucleotide entry and the additional automatically generated annotation.
The Entrez Cross-database Search Page lists, describes, and provides a link to each NCBI database. On this page, all NCBI databases can be searched simultaneously.
The European Bioinformatics Institute is in coalition with European Molecular Biology Laboratory. Their site has a large number of searchable databases of nucleotide sequences, protein sequences and protein structures.
This proteomics server from the Swiss Institute of Bioinformatics includes PROSITE, ENZYME, and GermOnLine, as well as other databases. There are also links to tools and software packages that can be downloaded and used for proteomics and sequencing.
The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures. ExPASy Translate is a tool that translates a DNA or RNA sequence to a protein sequence.
The Experimental Factor Ontology (EFO) is an application focused ontology modeling the experimental factors in ArrayExpress. The ontology has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data.
The FGPP site allows for searching of databases, including BLAST, protein families, and knockouts as well as protein scanning, and predicting myristoylation sites, all in relation to plant phosphorylation.
IMGT, the international ImMunoGeneTics information system, is an integrated knowledge resource specialized in the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF), major histocompatibility complex superfamily (MhcSF) and related proteins of the immune system (RPI) of human and other vertebrate species.
The Integr8 web portal provides easy access to integrated information about deciphered genomes and their corresponding proteomes. Available data includes DNA sequences (from databases including the EMBL Nucleotide Sequence Database, Genome Reviews, and Ensembl); protein sequences (from databases including the UniProt Knowledgebase and IPI); statistical genome and proteome analysis (performed using InterPro, CluSTr, and GOA); and information about orthology, paralogy, and synteny.
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a database of biological systems, consisting of genetic building blocks of genes and proteins (KEGG GENES), chemical building blocks of both endogenous and exogenous substances (KEGG LIGAND), molecular wiring diagrams of interaction and reaction networks (KEGG PATHWAY), and hierarchies and relationships of various biological objects (KEGG BRITE). KEGG provides a reference knowledge base for linking genomes to biological systems and also to environments by the processes of PATHWAY mapping and BRITE mapping.
In the LGIC Database you will find the nucleic acid and protein sequences of ligand-gated ion channel subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Finally, the atomic coordinates of subunits, or portion of subunits, are provided when available.
MaizeGDB, funded by USDA Agricultural Research Service, is the community database for biological information about the crop plant Zea mays ssp. mays. The following datatypes are accessible through this site: genetic, genomic, sequence, gene product, functional characterization, literature reference, and person/organization contact information.
MicroRNAs (miRNAs) are small noncoding RNA molecules, which are capable of negatively regulating gene expression to control cellular mechanisms. miRNAMap is a database of experimental verified microRNAs and experimental verified miRNA target genes in human, mouse, rat, and other metazoan genomes.
MAST is a tool for searching biological sequence databases for sequences that contain one or more of a group of known motifs.
Mouse genome Informatics provides accessible data to laboratory mouse genetics, genomics and biology.
The NDB’s goal is to provide access to nucleic acid structure. The services include an atlas that provides multiple X-ray and NMR images, areas were data can be deposited and downloaded, and a search function.
Published by Oxford Journals Online, Nucleic Acids Research Journal gives access to full text articles from 1996 to the current issue, with abstracts available as far back as 1975, as well as the annual database issue.
The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
This register is an electronic publication for articles describing the isolation and DNA sequencing of plant genes. The site is searchable with full text reports from 1995-2000.
The RNA Modification Database is an updated and comprehensive listing of post-transcriptionally modified nucleosides from RNA. It is searchable by various parameters including base type and RNA source.
The RNase P Database is a collection of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and additional information.
The Yeast Genome site provides a variety of tools, such as BLAST, PatMatch, gene sequencing resources and chromosomal features search, which can be applied to the S.cerevisiae genome.
The S.pombe genome project allows searching of the genome, including all protein coding genes, psuedogenes, transposons, and tRNAs. Also included are sequence searches and cloning resources.
Sequence Motif search will search through motif libraries online to see if the protein or nucleic acid sequence entered contains any motifs and identifies them.
The SILVA databases are maintained by the Microbial Genomics Group at the Max Planck Institute (MPI) for Marine Microbiology, in cooperation with the Department of Microbiology at the Technical University of Munich and Ribocon. The web resource provides quality checked and regularly updated databases of aligned SSU (small subunit) and LSU (large subunit) ribosomal RNA (rRNA) sequences. These databases can be used for rapid rRNA sequence retrieval, phylogenetic analysis, and the design of probes and primers for diversity analysis. They are fully compatible with the software package ARB.
This page, maintained by the European Bioinformatics Institute, lists various sequence database similarity search tools such as FASTA, BLAST, MPsrch and ScanPS. Interactive as well as email submissions are available for each of these services.
The Stanford bioinformatics resource provides workshops, consultations, hardware and software access for various computers and systems for use in Biomedical research.
The Stanford Genome Technology center provides information on the cost-effectiveness of DNA sequencing, and about the genome of S. Cerevisiae. The site also offers publications and project information.
The Stanford Microarray Database (SMD) is a research tool and archive that allows researchers to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML. Registration is required and fees may apply.
TIGR databases contains genomic information for over 20 microbial species, with extensive publication information for each genome.
The Zebrafish Information Network is a comprehensive database on everything there is to know about Zebrafish, including transgenics, wild-type lines, genes, gene expression, genetics maps and publications.
Encyclopedias
NCBI Entrez Resources
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
Entrez searches the National Center for Biotechnology Information (NCBI) databases to provide integrated access to nucleotide and protein sequence data from over 160,000 species, along with three-dimensional protein structures, genomic mapping information, PubMed MEDLINE, and more. Sequence data are combined from various sources, including GenBank, EMBL, DDBJ, RefSeq, PIR-International, PRF, Swiss-Prot, and PDB. Entrez can be searched with a wide variety of text terms such as author name, journal name, gene or protein name, organism, unique identifier (e.g., accession number, sequence ID, PubMed ID), and other terms, depending on the database being searched.
3D Domains are compact structural domains identified automatically in MMDB, Entrez's macromolecular three-dimensional structure database. 3D Domains are the units of comparison for structure neighbor calculations using the VAST algorithm. Links to VAST or 3D Domain neighbors display 3D Domains (and complete polypeptide chains) with similar 3D structures.
The BioSystems database contains records that group together molecules that interact in biological systems. One type of biosystem is a biological pathway, which can consist of interacting genes, proteins, and small molecules. Another type of biosystem is a disease, which can involve components such as genes, biomarkers, and drugs.
In collaboration with authors and publishers, the National Center for Biotechnology Information (NCBI) is adapting biomedical Books for the web.
Cancer Chromosomes contains three cancer cytogenetic databases: the NCI Mitelman Database of Chromosome Aberrations in Cancer, the NCI Recurrent Chromosome Aberrations in Cancer, and the NCI and NCBI SKY/M-FISH & CGH Database. Karyotype, SKY/M-FISH, and CGH data can be searched simultaneously. Similarity searches demonstrate cytogenetic and clinical relatedness at varying levels of specificity.
CDD currently contains domains derived from two popular collections, Smart and Pfam, plus contributions from colleagues at NCBI, such as COG. The source databases also provide descriptions and links to citations. Since conserved domains correspond to compact structural units, CDs contain links to 3D-structure via Cn3D whenever possible.
The Entrez Cross-database Search Page lists, describes, and provides a link to each NCBI database. On this page, all NCBI databases can be searched simultaneously.
The database of genotype and phenotype (dbGaP) stores phenotype and genotype data, as well as the associations between them. Studies generating data for dbGaP will include genome-wide association studies, medical sequencing, and molecular diagnostic assays. Summaries of phenotype and genotype data as well as study documents and association analyses (when available) will be found on the public site. Authorized access may be required for downloading coded individual-level phenotypes genotypes and pedigrees.
The EST database contains all records found within the Expressed Sequence Tag (EST) division of GenBank. EST records contain first-pass single-read cDNA sequences and include no annotated biological features.
Gene organizes information about the characteristics and defining sequences of genes from species in Genome, RefSeq, and other model organisms.
The whole Genomes of over 1000 viruses and over 100 microbes can be found in Entrez Genome. The genomes represent both completely sequenced organisms and those for which sequencing is in progress. All three main domains of life - bacteria, archaea, and eukaryota - are represented, as well as many viruses and organelles.
Genome Project is a collection of complete and incomplete large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. The database is organized into organism-specific overviews that function as portals from which all projects in the database pertaining to that organism can be browsed and retrieved.
The GENSAT project aims to map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques. The GENSAT database contains mouse brain images at several different developmental stages using both techniques, with a searchable set of gene expression annotations.
Comparable experimental sample sets assembled from the Gene Expression Omnibus (GEO) repository. Entrez GDS queries all GEO DataSet annotation, allowing identification of experiments of interest.
Individual gene expression and molecular abundance profiles assembled from the Gene Expression Omnibus (GEO) repository. Entrez GEO Profiles queries annotation and pre-computed profile characteristics, allowing identification of specific genes, and molecular abundance profiles of interest.
Individual gene expression and molecular abundance profiles assembled from the Gene Expression Omnibus (GEO) repository. Entrez GEO Profiles queries annotation and pre-computed profile characteristics, allowing identification of specific genes, and molecular abundance profiles of interest.
The GSS database contains all records found within the Genome Survey Sequence (GSS) division of GenBank. GSS records contain first-pass single-read genomic sequences and rarely include annotated biological features.
HomoloGene is an automated system for detecting homologs among the annotated genes of several completely sequenced eukaryotic genomes.
The Entrez Journals database searches for a journal and has links to records for that journal in the databases. The Journals database can be searched using the journal title, MEDLINE abbreviation, NLM ID, ISO abbreviation, or ISSN. The database includes the journals in all Entrez databases, e.g., PubMed, Nucleotide, Protein.
MeSH is NLM's controlled vocabulary used for indexing articles in PubMed. MeSH terminology provides a consistent way to retrieve information that may use different terminology for the same concepts. Use the MeSH database to build a PubMed search strategy.
The Nucleotide database contains records for all Entrez Nucleotide sequences that are not found within the Expressed Sequence Tag (EST) or Genome Survey Sequence (GSS) divisions of GenBank. These include sequences from all remaining divisions of GenBank, NCBI Reference Sequences (RefSeqs), Whole Genome Shotgun (WGS) sequences, Third Party Annotation (TPA) sequences, and sequences imported from the Entrez Structure database.
Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in animal species (other than human and mouse) authored by Professor Frank Nicholas of the University of Sydney, Australia, with help from many people over the years. The database contains textual information and references, as well as links to other relevant records.
Online Mendelian Inheritance in Man (OMIM) is a catalog of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases. It is based on the book, Mendelian Inheritance in Man. The online version is updated daily. The OMIM FAQs provide additional information about the book and the online database.
Peptidome a repository of tandem mass spectrometry peptide and protein identification data generated by the scientific community.
PopSet is a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population. The population could originate from different members of the same species, or from organisms from different species. They are submitted to GenBank via Sequin, often as a sequence alignment.
The Probe Database is a public registry of sequence-specific reagents designed for use in a wide variety of biomedical research applications, together with information on reagent availability, experimental protocols, probe effectiveness, and computed sequence similarities.
The Protein entries in the Entrez search and retrieval system have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.
Protein Clusters is a collection of related protein sequences (clusters). Currently it consists of Reference Sequence proteins encoded by complete prokaryotic and chloroplast genomes and plasmids. This database contains both curated and non-curated clusters.
SNP is NCBI’s database of Single Nucleotide Polymorphisms.
SRA is a database of raw sequence data from sequencing instruments.
Structure: The Molecular Modeling Database (MMDB) contains 3-D macromolecular structures, including proteins and polynucleotides. MMDB contains over 20,000 structures and is linked to the rest of the NCBI databases, including sequences, bibliographic citations, taxonomic classifications, and sequence and structure neighbors.
UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.
UniSTS is a NCBI resource that reports information about markers, or Sequence Tagged Sites (STS). UniSTS integrates marker and mapping data from public resources including GenBank, RHdb, GDB, various human maps (Genethon genetic map, Marshfield genetic map, Whitehead RH map, Whitehead YAC map, Stanford RH map, NHGRI chr 7 physical map, WashU chrX physical map), various mouse maps (Whitehead RH map, Whitehead YAC map, Jackson laboratory's MGD map).
The Map Viewer provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows you to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. The number and types of available maps vary by organism. If multiple maps are available for a chromosome, Map Viewer displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system.
The NCBI Taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence.
PubChem BioAssay contains the results of biological activity screening from a variety of public sources. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to that screening procedure. PubChem BioAssay results are linked to PubChem Substance, and in turn to PubChem Compound, whenever chemical structures are known. Screening results may be browsed via a web interface and also downloaded for further cheminformatics analysis.
PubChem Compound contains chemical structure information drawn from a variety of public sources. Compounds may be searched by chemical properties and are pre-clustered into identity and similarity groups by structure comparison. Whenever possible, compounds are linked via PubChem Substance to information on their biological activities. Available links include PubMed citations, protein 3D structures and links to biological screening results available in PubChem BioAssay.
PubChem Substance contains descriptions of chemical samples, from a variety of public sources, and links to information on their biological activities. The description includes links to PubChem Compound in cases where the chemical structures of compounds in the sample are known. Links providing information on biological activity include links to PubMed citations, protein 3D structures, and to biological screening results available in PubChem BioAssay.
Developed by the National Center for Biotechnology Information (NCBI), Pubmed is a free version of MEDLINE that offers links to GenBank records, other molecular sequence data, and other resources. MEDLINE, produced by the National Library of Medicine, is an index to journal articles in medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences, including both basic biomedical sciences and clinical practice. It indexes over 4,000 journals. The database contains citations from 1950 to the present with some older citations. An important feature of MEDLINE is the use of Medical Subject Headings (MeSH), a powerful tool for searching specific topics or for comprehensive general searches. MEDLINE is also available to Stanford users via EBSCO, ISI Web of Knowledge, NLM Gateway, OCLC ,and Ovid.
PubMed Central (PMC) is the U.S. National Library of Medicine's digital archive of life sciences journal literature. Access to the full text of articles in PMC is free, except where a journal requires a subscription for access to recent articles.