Biologia molecolare - il sistema Entrez

Il sistema Entrez

• OMIM
• PubMed
• Giornali elettronici
• Mappe e genomi
• Sequenze proteiniche
• Sequenze nucleotidiche
• Strutture 3D
• Tassonomia

Il sistema Entrez

• OMIM
• PubMed
• Giornali elettronici
• Mappe e genomi
• Sequenze nucleotidiche
• Strutture 3D
• Sequenze proteiche
• Tassonomia

NCBI

Databases

Search Entrez for

Entrez is the text-based search and retrieval system used at NCBI for the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others.

The complete list of Entrez databases can be viewed in the search pulldown menu.

Nucleotide Databases

• dbEST
• dbGSS
• dbSNP
• MGC
• PopSet
• RefSeq

Entrez is a retrieval system for searching several linked databases. It provides access to:

• PubMed: The biomedical literature (PubMed)
• Nucleotide: sequence database (GenBank)
• Protein: sequence database
• Structure: three-dimensional macromolecular structures
• Genome: complete genome assemblies
• PopSet: population study data sets
• OMIM: Online Mendelian Inheritance in Man
• Taxonomy: organisms in GenBank
• Books: BookShelf online books
• ProbeSet: gene expression and microarray datasets
• 3D Domains: domains from Entrez Structure
• UniSTS: markers and mapping data
• SNP: single nucleotide polymorphisms
• CDD: conserved domains
• Journals: journals in Entrez
• UniGene: gene-oriented clusters of transcript sequences
• PMC: full-text digital archive of life sciences journal literature
• NCBI Web Site: NCBI Web site search

Pre-computed similarity searches are available for most database records, which produce a list of related sequences, structure neighbors, as well as related articles.

NCBI's Protein Sequence Information Survey Results

The Entrez search and retrieval system is provided by the National Center for Biotechnology Information. NCBI also builds, maintains, and distributes the GenBank sequence database.

Revised: March 27, 2003

Disclaimer | Write to the Help Desk NCBI | NLM | NIH

Database pull-down menu

The Entrez Nucleotides database is a collection of sequences from several sources, including GenBank, RefSeq, and PDB. The number of bases grows at an exponential rate. Today's total is:

The search query box appears directly adjacent the "Search" pull-down menu. Search terms are typed into this box and executed by selecting the "Go" button (or by pressing the "return" button on your computer keyboard). The "Clear" button erases search terms in the query box. Use it to begin a new search.

There are links, on the feature bar, to Limits, Preview/Index, History, and Clipboard below the search query box. These are defined in this introduction and summarized in the Summary Matrices at the end of this introduction. See also the Using Limits, Using Preview/Index, Using Your History, and Details Button, Add To Clipboard, and Save sections of this document for more information.

The Databases

Nucleotide Database

The Nucleotide database contains sequence data from GenBank, EMBL, and DDBJ, the members of the tripartite, international collaboration of sequence databases. EMBL is the European Molecular Biology Laboratory (EMBL) at Hinxton Hall, UK. DDBJ is the DNA Database of Japan (DDBJ) in Mishima, Japan. Sequence data is also incorporated from the Genome Sequence Data Base (GSDB), Santa Fe, NM. Patent sequences are incorporated through arrangements with the U.S. Patent and Trademark Office (USPTO), and via the collaborating international databases from other international patent offices.

Nucleotide Databases

• dbEST
• dbGSS
• dbSNP
• dbSTS
• Nucleotide
• GenBank
• HomoloGene
• MGC
• PopSet
• RefSeq
• TPA
• Trace Archive
• UniGene
• UniSTS

Protein Databases

• Domains
• Proteins
• PROW
• RefSeq

Structure Databases

• Domains
• 3D Domains
• Structure (MMDB)

Taxonomy Databases

• Taxonomy

Genome Databases

• Genomes
• Gene
• LocusLink
• COGs

Expression Databases

• GEO
• GEO Datasets
• SAGE

Revised: January 8, 2004.

Bookshelf

Look for background information or research new topics with freely accessible, online biomedical textbooks. The growing NCBI Bookshelf can be searched directly or accessed via PubMed abstracts by clicking the "Books" link. The database can also be searched by choosing "Books" from the Entrez pull-down menu.

PubMed

Through PubMed, anyone can access MEDLINE's 11,000,000 biomedical journal citations to research biomedical questions. Clicking the "Related articles" link for each abstract can expand your search. Click here for the PubMed tutorial.

PubMed Central

PubMed Central is a digital archive of life sciences journal literature. Integrated into the Entrez retrieval system, PMC provides free and unrestricted access to the full text of over 100 life sciences journals, with more to come.

Online Mendelian Inheritance in Man (OMIM)

With over 14,000 entries, OMIM, maintained by Dr. Victor A. McKusick and his colleagues at Johns Hopkins University, represents a comprehensive and constantly updated catalog of inherited diseases.

The Bookshelf is a growing collection of biomedical books that can be searched directly by typing a concept into the textbox above and selecting “Go”. Try one of these searches:

• cell cycle control
• immunodeficiency
• protein evolution

Books are also linked to terms in PubMed abstracts: when viewing an abstract, select the “Books” link to see phrases within the abstract hyperlinked to book sections.

Updated on the Bookshelf:

• Annual Reviews Collection [Internet]. Twelve articles reproduced from the Annual Reviews Series. Bethesda (MD): National Library of Medicine (US), NCBI; 2002 Nov.

New on the Bookshelf:

• Genomes. 2nd ed. Brown, T. A. Oxford, UK: BIOS Scientific Publishers Ltd; 2002.
• Human Molecular Genetics 2. 2nd ed. Strachan, Tom and Read, Andrew P. Oxford, UK: BIOS Scientific Publishers Ltd; 1999.

Book List

• Annual Reviews Collection [Internet]. Twelve articles reproduced from the Annual Reviews Series. Bethesda (MD): National Library of Medicine (US), NCBI; 2002 Nov.
• Basic Neurochemistry, Molecular, Cellular, and Medical Aspects. 6th ed. Siegel, George J.; Agranoff, Bernard W.; Albers, R. Wayne; Fisher, Stephen K.; Uhler, Michael D. Philadelphia: Lippincott Williams & Wilkins; 1999.

14 items in Modern Genetic Analysis.

Griffiths, Anthony J.F.; Gelbart, William M.; Miller, Jeffrey H.; Lewontin, Richard C.New York: W H Freeman & Co; c1999.

11 items in Medical Microbiology. 4th ed.

Baron, Samuel, editorGalveston: University of Texas Medical Branch; c1996.

11 items in Molecular Cell Biology. 4th ed.

Lodish, Harvey; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James E.New York: W H Freeman & Co; c2000.

9 items in The Cell - A Molecular Approach. 2nd ed.

Cooper, Geoffrey M.Sunderland, Massachusetts: Sinauer Associates, Inc; c2000

7 items in Introduction to Genetic Analysis. 7th ed.

Griffiths, Anthony J.F.; Miller, Jeffrey H.; Suzuki, David T.; Lewontin, Richard C.; Gelbart, William M.New York: W H Freeman & Co; c1999.

6 items in The Human ATP-Binding Cassette (ABC) Transporter Superfamily.

Dean, MichaelBethesda (MD): National Library of Medicine (US). NCBI; 2002 Nov.

6 items in Basic Neurochemistry, Molecular, Cellular, and Medical Aspects 6th ed.

Siegal, George J.; Agranoff, Bernard W.; Albers, R. Wayne; Fisher, Stephen K.; Uhler, Michael D., editorsPhiladelphia, Pennsylvania: Lippincott Williams & Wilkins; c1999.

4 items in Molecular Biology of the Cell. 3rd ed.

Alberts, Bruce; Bray, Dennis; Lewis, Julian; Raff, Martin; Roberts, Keith; Watson, James D.New York and London: Garland Publishing; c1994

3 items in Surgical Treatment

Holzheimer, Rene G.; Mannick, John A., editors;Munich: Zuckschwerdt Publishers; c2001

3 items in Cancer Medicine. 5th ed.

Bast, Robert C.; Kufe, Donald W.; Pollock, Raphael E.; Weichselbaum, Ralph R.; Holland, James F.; Frei, Emil, editors.Canada: BC Decker Inc; c2000

81 items in Cancer Medicine. 5th ed.Bast, Robert C.; Kufe, Donald W.; Pollock, Raphael E.; Weichselbaum, Ralph R.; Holland, James F.; Frei, Emil, III, editors.Hamilton (Canada): BC Decker Inc; c2000.

54 items in Medical Microbiology. 4th ed.Baron, Samuel, editor.Galveston (TX): University of Texas Medical Branch; c1996.

46 items in Human Molecular Genetics 2. 2nd ed.Strachan, Tom and Read, Andrew P.Oxford, UK: BIOS Scientific Publishers, Ltd; 1999.

41 items in Mapping Protein/DNA Interactions by Cross-Linking.Paris: Institut National de la Santé et de la Recherche Médicale; 2001.

29 items in Eurekah Bioscience Collection.Chapters taken from the Eurekah Bioscience database.Eurekah.com and Landes Bioscience; 2003.

23 items in Retroviruses.Coffin, John M.; Hughes, Stephen H.; Varmus, Harold E.Plainview (NY): Cold Spring Harbor Laboratory Press; c1997.

17 items in Molecular Cell Biology. 4th ed.Lodish, Harvey; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James.New York: W. H. Freeman & Co.; c2000.

6.2.3. A wide variety of PCR-based methods can be used to assay for known mutations

PCR is a very rapid and valuable tool for detecting pathogenic mutations and other mutations of interest. The examples below illustrate some popular methods.

Allelic discrimination by size or susceptibility to restriction enzyme

Small insertions or deletions (such as the three nucleotide deletion in the common cystic fibrosis (CFTR) allele, F508del) can be simply detected by designing primers from regions closely flanking the mutation site and distinguishing the normal and mutant alleles by size on polyacrylamide or agarose gels. If the mutation changes a restriction site, mutant and normal alleles can be distinguished by amplifying across the mutant site and digesting the PCR product with relevant restriction endonuclease, exactly as in Figure 6.6.

Allelic discrimination by susceptibility to an artificially introduced restriction site

Even if the mutation does not result in a restriction site difference, it may be possible to exploit the difference between normal and mutant alleles by amplification-created restriction site PCR. This is a form of mismatched primer mutagenesis (see Section 6.4.2) in which a primer is deliberately designed from sequence immediately adjacent to, but not encompassing, the restriction site. The primer is deliberately designed to have a mismatched nucleotide which together with the sequence of the mutant site creates a restriction site not present in normal alleles (see Figure 17.2 for a specific example).

Allele-specific PCR (ARMS test)

Oligonucleotide primers can be designed so as to discriminate between target DNA sequences that differ by a single nucleotide in the region of interest. This is a form of allele-specific PCR, the PCR equivalent of the allele-specific hybridization which is possible with ASO probes (Section 5.3.1). In the case of allele-specific hybridization, alternative ASO probes are designed to have differences in a central segment of the sequence (to maximize thermodynamic instability of mismatched duplexes). However, in the case of allele-specific PCR, ASO primers are designed to differ at the nucleotide that occurs at the extreme 3’ terminus. This is so because the DNA synthesis step in a PCR reaction is crucially dependent on correct base-pairing at the 3’ end (Figure 6.9). This method can be used to type specific alleles at a polymorphic locus, but has found particular use as a method for detecting a specific pathogenic mutation, the so-called amplification refractory mutation system (ARMS; Newton et al., 1989).

Mutation detection using the 5’ → 3’ exonuclease activity of Taq DNA polymerase

Correct base-pairing at the 3 end of PCR primers is the basis of allele-specific PCR.

Navigation

About this book

• 6. PCR, DNA sequencing and in vitro mutagenesis

• 6.1. Basic features of PCR
• 6.2. Applications of PCR
• 6.3. DNA sequencing
• 5.4. In vitro site-specific mutagenesis
• Further reading

Design allele-specific primers (nucleotides 1 - 17)

PCR with _ASP1 or _ASP2 + conserved primer (CON)

but

No amplification

Enter one or more search terms, or click Preview/Index for advanced searching.

• Enter author names as smith jc. Initials are optional.
• Enter journal titles in full or as MEDLINE abbreviations. Use the Journals Database to find journal titles.

PubMed, a service of the National Library of Medicine, provides access to over 12 million MEDLINE citations back to the mid-1960's and additional life science journals. PubMed includes links to many sites providing full text articles and other related resources.

Bookshelf Additions

The Eurekah Bioscience Collection is now available for interactive searching on the BookShelf.

PubMed E-mail Available

An e-mail selection has been added to the Send to pull-down menu.

New Icons

Icons display next to PubMed citations to indicate the following:

• No Abstract
• Abstract available
• Full-text article available free in PubMed Central.

http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=PubMed

Items 1-20 of 21183

1. Cobb BR, Fan LJ, Kovacs TFI, Sorscher EJ, Clancy JP.

   Adenosine Receptors and Phosphodiesterase Inhibitors Stimulate Cl- Secretion in Calu-3 Cells.

   Am J Respir Cell Mol Biol. 2003 Apr 24 [epub ahead of print]

   PMID: 12714375 [PubMed - as supplied by publisher]

2. Kothe M, Antl M, Huber B, Stoecker K, Ebrecht D, Steinmetz L, Eberl L.

   Killing of Caenorhabditis elegans by Burkholderia cepacia is controlled by the cep quorum-sensing system.

   Cell Microbiol. 2003 May;5(5):343-51.

   PMID: 12713492 [PubMed - in process]

3. Bramanti B, Hummel S, Chiarelli B, Herrmann B.

   Ancient DNA analysis of the delta F508 mutation.

   Hum Biol. 2003 Feb;75(1):105-15.

   PMID: 12713151 [PubMed - in process]

4. Rubin BK.

   Cystic fibrosis: Bench to bedside 2003.

   Can Respir J. 2003 Apr;10(3):161-4. No abstract available.

   PMID: 12712228 [PubMed - in process]

5. Fong P, Argent BE, Gueuino WB, Gray MA.

   Characterization of Vectorial Chloride Transport Pathways in the Human Pancreatic Duct Adenocarcinoma Cell Line, HPAF.

   Am J Physiol Cell Physiol. 2003 Apr 23 [epub ahead of print]

   PMID: 12711595 [PubMed - as supplied by publisher]

6. Pardo E, Iapichino L, Collura M, Furnari ML, Termini L, Cascio A, Giordano S.

   [Anti-Pseudomonas aeruginosa antibodies and lung disease in cystic fibrosis]

   Infez Med. 2000;8(2):87-91. Italian.

   PMID: 12709601 [PubMed - as supplied by publisher]

7. Sui W, Boyd C, Wright JT.

   Altered pH Regulation During Enamel Development in the Cystic Fibrosis Mouse Incisor.

   J Dent Res. 2003 May;82(5):388-92.

   PMID: 12709507 [PubMed - in process]

8. Akalin F, Korolbeyre U TF, Bakac S, DaGil E.

   Effects of childhood bronchiectasis on cardiac functions.

   Pediatr Int. 2003 Apr;45(2):169-174.

   PMID: 12709143 [PubMed - in process]