NCBI News

National Center for Biotechnology Information

National Library of Medicine National Institutes of Health Fall 1999

Entrez Search Services Enhanced NCBI Home Page

NCBI’s popular search serv- base field. Although field specifi- Redesigned ice has been overhauled to accom- cation has always been available modate additional data resources and in Entrez, the new release has two NCBI’s recently reorganized home facilitate more finely tuned searches major changes. First, commonly page is designed to better accom- demanded by the explosion of data used field restrictions, such as modate its growing set of resources. in the sequence, structure, and liter- Molecule Type for DNA sequences Since 1994, when the Web site was ature databases. The new Entrez and Language for PubMed searches, launched, the number of services not only offers an enhanced search are listed for each Entrez data- has grown from 4 to almost 40! The interface to the five familiar data- base and can be selected easily new design not only offers the need- bases—Nucleotide, , Struc- from pull-down menus. Commonly ed flexibility and organization, but ture, Genome, and PubMed—but desired data exclusions,such as also provides added interest through also adds a sixth database, PopSet EST and STS sequences, are easily frequently updated announcements for population studies, to the mix. invoked by checking a box. Second, and news items. limits can be applied globally to Central to the new interface is a all searches of a particular data- The new page retains the familiar standard query box on every page base, relieving you of having to top row of buttons for prominent that allows you to select a target incorporate the same restrictions access to the most frequently used database and initiate a new search repeatedly in multiple iterations resources—and adds a new query from anywhere within Entrez, of the searching process. box that launches searches of making it easier to move from data- GenBank, PubMed, and other data- base to database. The new Entrez Just as data fields vary from database bases directly from the home page. also offers several features for com- to database within Entrez, the para- Continued on page 8 posing detailed search queries and meters available for limiting are also managing the results, including database-dependent. For example, In this issue Limits, Index, History, and Clip- limits unique to PubMed include Pub- board. These options can be select- licationType and Language. Limits 1 Enhanced Entrez ed from every Entrez page, just for the Nucleotide and Protein data- 1 New Home Page below the query box.Detailed docu- bases include Location and 3 Cn3D 2.5 mentation, including search exam- Modification Date, among others. 4 News Briefs ples, is available from a Helplink 4 GenBank Contig Division on all Entrez pages. Index: Browsing Available 5 VecScreen Search Terms 5 Recent Publications Limits: Setting Field Restrictions The Index option allows you to 6 BLASTLab The Limits feature is used to restrict browse the alphabetical indexes of 7 Frequently Asked Questions a search term to a particular data- Continued on page 2 Entrez Search Services Clipboard: NCBINews Continued from page 1 Collecting Search Results The Clipboard serves as a collection search terms in each field of the bin for search results. It allows you Entrez databases. This is the same to save some or all of the documents NCBI Newsis distributed four times a year. We welcome communication basic functionality that was provi- retrieved from many separate from users of NCBI databases and ded through the List Terms search searches as you go along. Items are software and invite suggestions for mode in earlier versions of Entrez, placed on the Clipboard by check- articles in future issues. Send corre- spondence to NCBI News at the with some improvements in ease ing a selection box next to their address below. of use. As you browse, you can item number. Multiple items may be

NCBI News select and search the terms you checked in this manner and then National Library of Medicine find. Compound searches can be added to the Clipboard with a single Bldg. 38A, Room 8N-803 constructed by choosing terms click. Alternatively, an entire set 8600 Rockville Pike iteratively from the Index list, and of resultscan be saved at once by Bethesda, MD 20894 Phone: (301) 496-2475 combining them by using one of clicking on Add to Clipboard. Fax: (301) 480-9241 three logical operator buttons Separate Clipboards are maintained E-mail: [email protected] provided: AND, OR, orNOT. for each database, and contentsare Editors removedafter 1 hour of inactivity. Dennis Benson Barbara Rapp History:

Contributors Recording Previous Searches PopSet: Adding a New Mark Cavanaugh Ilene Mizrachi Entrez Database Paul Kitts Steve Sherry The new Entrez automatically Tom Madden Yanli Wang retains a search history that can be The new PopSet database is avail- Margaret McGhee used to build up a very selective able only under the new release Writer search from a combination of prev- of Entrez. It can be selected in the David Wheeler ious searches. The History extends same manner as the other data- Editing, Graphics, and Production back to a maximum of 100 searches bases, that is, from the list box next Marla Fogelman per Entrez session and expires after to the main query box if you want Veronica Johnson Jennifer Vyskocil about 1 hour of inactivity. The His- to launch a search directly from tory is presented as a table giving, another database, or from the top Design Consultant Gary Mosteller for each search, a search number, row of database names if you want the search query, the time of the to go to the PopSet home page. In 1988, Congress established the National Center for Biotechnology search, and the number of database Information as part of the National hits. Clicking on the number of hits PopSet contains aligned nucleotide Library of Medicine; its charge is recalls the results of the search. The or protein sequences submitted as to create information systems for a set resulting from a population, molecular biology and genetics search number can be entered into a phylogenetic, or mutation study. data and perform research in the query box as a substitute for the These kinds of populations sets computational molecular biology. literal query and may be considered are useful in describing such events The contents of this newsletter may a variable. To combinesearches “#1” as evolution and population be reprinted without permission. and “#2” and retrieve their intersec- The mention of trade names, com- variation. — MM, BR, DW tion, simply enter “#1 AND #2” mercial products, or organizations does not imply endorsement by into the main query box. This result Both new and old interfaces are NCBI, NIH, or the U.S. Government. becomes Search History entry #3 running in parallel during an initial NIH Publication No. 99-3272 and may be used to construct other testing phase. To try the new Entrez, searches by using “#3” in place of ISSN 1060-8788 click on the prominent green ellipse ISSN 1098-8408 (Online Version) the actual query. A separate History atop the Entrez home page. is maintained for each database.

Fall1999 NCBI News 2 Cn3D 2.5 Offers Feature Editing and Global Save Figure 2 NCBI has recently released version ment was produced 2.5 of the Cn3D macromolecular by NCBI’s Vector structure viewer. PC users will enjoy Alignment Search a smooth, single-click installation Tool (VAST) and process and all users will appreciate downloaded by Cn3D the usability enhancements in this from the Molecular latest release. Modeling Database (MMDB). The dark- Cn3D 2.5 offers a greatly expanded colored residues are array of annotation tools, including those of the bacter- the ability to define molecular fea- iophage T4 enzyme tures and specify their display char- with PDB code acteristics. Greater control over “1TFR,”1and the every aspect of the molecular display light-colored residues is facilitated through four control are those of the T5 panels, which govern molecular col- enzyme with PDB code “1EXN.”2 The or schemes, visibility, rendering, and Cn3D Feature panel showing custom rendering settings for the labeling. After a molecule, or set of two dark spheres four catalytic acidic residues of the user-defined “t4_cat” feature. molecules, has been rendered and represent catalytically annotated, the entire ensemble of important magnesium coordinate data and display specifi- ions present in the 1TFR structure. dow, shown in Figure 2, was then cations can be saved for later view- The 1TFR and 1EXN exonucleases used to give the selected residues a ing or transmittal to colleagues. are responsible for removing RNA feature name and define their display primers used during bacteriophage and visibility properties. These new annotation features are DNA replication. illustrated below, based on an exam- The alignment, rendering settings, ple from the online Cn3D tutorial. To generate this view, the alpha car- and user-defined features, “t4_cat” Figure 1 shows the area of the active bon traces of the default Cn3D Neigh- and “t5_cat,” can be saved in a single site of two structurally aligned 5´-3´ bor representation have been turned filefor later retrieval by usingthe exonucleases. The structural align- off, and two groups of aminoacids new Global Savefunction provided have been defined as “Features”and by the File/Save/Allmenu option. Figure 1 independently rendered as “fat tubes.” This rendering mode reveals the Cn3D is a project of NCBI’s Molec- excellent alignment of the corres- ular Structure research group, ponding side chains in the two struc- headed by Steve Bryant. The new tures. The background color was features in release 2.5 were devel- also changed from its default of oped primarily by NCBI scientists black to gray, another new option in Yanli Wang, Lewis Geer, Colombe Cn3D 2.5, using the Optionsmenu. Chappey, and Jonathan Kans.

Features were defined and given To download or read more about independent rendering and visibility Cn3D, visit www.ncbi.nlm.nih.gov/ settings using the Viewer Controls Structure/CN3D. — DW, YW window. To define the feature “t4_cat,” for instance, 1TFR residuesD19, D71, Notes D132, and D155 were first selected in 1. Mueser, TC, et. al. Cell85(7):1101–12, 1996. Cn3D view of structural alignment of the Sequencewindow. The Feature 2. Ceska, TA, et. al. Nature382(6586): 1EXN and 1TFR, as restricted by user- panel of the Viewer Controlswin- 90–3, 1996. specified features.

3 Fall1999 NCBI News GenBank Adds NewsBriefs NewsBriefs CON Division for Assembly Data DrosophilaSequence Submitting GSS Sequences Gets 40-Megabase Boost After January 1, 2000, GenBank will from Celera GenBank, EMBL, and DDBJ have es- no longer process Genome Survey tablished a special-purpose division, The complete Drosophila melanogaster Sequence (GSS) submissions made sequence is near completion. Currently, with BankIt or Sequin. Instead, use Contig (CON),for exchanging assem- GenBank contains 40 million base the custom GSS submission proce- bly instructions for data in the inter- pairs of finished Drosophilagenomic dures (www. ncbi.nlm.nih.gov/dbEST/ national DNA sequence databases. sequence from the NIH-funded Berke- how_to_submit.html. The e-mail The CON division contains no se- ley DrosophilaGenome Project and the address for GSS submissions is: European DrosophilaGenome Project. batch- [email protected]. quence data, but rather instructions An additional 100 million base pairs for the assembly of sequence data of unfinished sequence, including over Standalone BLAST 2.0.10 from multiple GenBank records. 600 BACs from the Berkeley project, are in the HTG division of GenBank. The latest version of Standalone BLAST DNA sequence records in GenBank Recently, Celera Genomics submitted is the first to include a standalone another 10 million base pairs of unfin- version of BLAST 2 Sequences (called (as well as EMBLand DDBJ) are cur- ished contigs, also in the HTG division. bl2seq). Standalone BLAST 2.0.10 also rently limited to 350 kb for flexibility To BLAST against these new sequences, allows searches of multiple databases, in data exchange, analysis, searching, select the HTGS database from the which circumvents two current limits Advanced BLAST page, and restrict the on database size—a maximum of 2 and display. Sequences that exceed search to Drosophila melanogaster gigabytes for any database and a 350 kb are split into multiple smaller using the organism filter box. maximum of 4 billion base pairs for records with separate accession num- nucleotide databases. Databases that bers. The CON division contains More dbSNP Data by FTP exceed these limits can now be format- ted as a series of smaller “volumes” information on how to reassemble NCBI now provides the full dbSNP using the program formatdb, also the full-length contig. It also includes database in three formats: flatfile, included in the BLAST 2.0.10 package. instructions for constructing assem- FASTA, and SQL DDL/table dumps. The blastall program performs the blies of non-contiguous sequence Complete copies of the database will multidatabase search. be refreshed weekly. See the README shown in Entrez as “segmented sets.” file for a complete description of the COGs Includes 21 Genomes various formats (ftp://ncbi.nlm.nih.gov/ General users of GenBank and Entrez snp/00readme). Clusters of Orthologous Groups should notice no changes in the (COGs) now incorporates 21 complete services. This data has been present Human Contig Breaks genomes, tripling the number of 10-Megabase Barrier organisms initially represented. In in the ASN.1 format and implemented addition to phylogenetic patterns, in Entrez for some time. The CON A segment of DNA sequence from the COGs may now be searched using division simply formalizes proce- 22 has become the first free-text words or protein and gene human continuous sequence over names. PSI-BLAST searches may be dures in development over the past 10 Mb in length. The Sanger Centre, launched using a set of similar seq- few years, and makes the assembly Washington University, and the uences from the COGs database to information available in a more University of Oklahoma contributed to construct a position-specific scoring this sequence. See the list of contigs for familiar format to users who down- matrix (PSSM). This PSSM can then be human chromosome 22 on NCBI’s used to search for remote homologs. load the GenBank database. Sequencingpage. The CON division will be available BLAST E-Mail Server UniGene for Zebra Fish with the December 15, 1999 release The BLAST e-mail server has been The zebra fish(Danio rerio)has been of GenBank. It applies only to upgraded to use the new QBLAST sys- added to the UniGene lineup. Over tem. The server therefore no longer sequence data as deposited in 5,600 zebra fish clusters are represent- supports BLAST 1.4 searches or the ed. Zebra fish joins the human, mouse, GenBank, EMBL, or DDBJ. It is RIPEM encryption software. and rat versions of UniGene. not being used for other genome assembly projects. — BR, DW

Fall1999 NCBI News 4 VecScreen: Selected Recent BLAST the Vector Out of Your Sequence Publications by NCBI Staff (GenBank Indexers Say “Use It!”)

Boeke, JD, and OK Pickeral. Retro- VecScreen is a system for quickly identifying segments of a nucleic acid shuffling the genomic deck. Nature 398(6723):108–9, 111, 1999. sequence that may be of vector origin. VecScreen was originally developed at NCBI for the GenBank Annotation Staff, who use it to verify that Copley, RR, J Schultz, CP Ponting, sequences submitted for inclusion in the database are free from contam- and P Bork. Protein families in multi- cellular organisms. Curr Opin Struct inating vector sequence. It is now available to the research public through Biol 9(3):408–15, 1999. the VecScreen Web site to help researchers identify and remove any segments of vector origin prior to sequence analysis or submission. Early Gladyshev, VN, M Krause, XM Xu, KV Korotkov, GV Kryukov, QA Sun, BJ identification of any foreign segments can avert erroneous conclusions Lee, JC Wootton, and DL Hatfield. about the biological significance of the sequence, prevent time and effort Selenocysteine-containing thioredoxin from being wasted in analysis of contaminated sequence, and speed the reductase in C. elegans.Biochem Bio- phys Res Commun259(2):244–9, 1999. release of the sequence in a public database. Hahn, T, E Matala, C Chappey,and N Ahmad. Characterization of mother- The UniVec Database infant HIV type 1 gagp17 sequences associated with perinatal transmission. VecScreen performs an optimized blastn search, with the sequence to be AIDS Res Hum Retroviruses screened as the query, of a specialized non-redundant vector database 15(10):875–88, 1999. called UniVec. Screening against UniVec is efficient because a large number Kondrashov, AS, and FA Kondrashov. of redundant subsequences have been eliminated to create a database Interactions among quantitative traits with only one copy of every unique sequence segment from a large number in the course of sympatric speciation. Nature400(6742):351–4, 1999. of vectors. In addition to vector sequences, UniVec contains sequences for those adapters, linkers, and primers commonly used in the process of Krizman, DB, L Wagner, A Lash, R cloning cDNA or genomic DNA. This enables detection of contamination Strausberg, and MR Emmert-Buck. Cancer Genome Anatomy Project: EST with these oligonucleotide sequences during the vector screen. Elimination sequencing and the genetics of cancer of redundant sequence segments reduces UniVec to less than 15% of the progression. Neoplasia 1(2):101–6, size of an equivalent database containing the full sequences for the same 1999. set of vectors. UniVec also uses a “pseudo-circularization” process, Leipe, DD, L Aravind, and EV appending the first 49 bases of a circular vector sequence to the end of the Koonin.Did DNA replication evolve Nucleic Acids vector to avoid missing a match due to end effects. The current version of twice independently? Res 27(17):3389–401, 1999. UniVec represents 971 vector and oligonucleotide sequences. To see the sequences used to build the database, go to the UniVecRepresentation Matsuo, Y,andSH Bryant. Identifi- cation of homologous core structures. List, accessible from the VecScreen page. Proteins35(1):70–9, 1999.

Wolf, YI, L Aravind, andEV Koonin. The VecScreen Graphic Rickettsiaeand Chlamydiae: evidence of horizontal gene transfer and gene ex- The blastn output from VecScreen is summarized using a graphical repre- change. Trends Genet15(5):173–5, 1999. sentation of the query sequence, which is color-coded to show the location of segments that match vector sequences. The matches are color-coded at Zaman, V, M Zaki, J Howe, M Ng, DD Leipe, ML Sogin, and JD Silberman. four levels of significance: strong, moderate, weak, and suspicious. Hyperamoebaisolated from human feces: description and phylogenetic Give VecScreen a try at www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html. affinity. Eur J Protistol35(2):197c– 207, 1999. — PK, DW

5 Fall1999 NCBI News Using the New QBLAST Reformatting Feature to Detect Conserved Amino Acids

One of the strengths of the recently Score E implemented QBLAST system is Sequences producing significant alignments: (bits) Value its ability to generate output quickly in any of several formats sp|P36925|IL8_SHEEP INTERLEUKIN-8 PRECURSOR (IL-8) >gi|5431... 96 7e-22 after a search has been completed. sp|P79255|IL8_BOVIN INTERLEUKIN-8 PRECURSOR (IL-8) >gi|1699... 93 4e-21 Choosing one of the Master-Slave emb|CAA43461| (X61151) interleukin-8 [Sus scrofa] 92 6e-21 alignment formats, rather than the pir||A44253 alveolar macrophage chemotactic factor-I (AMCF-... 92 6e-21 default Pairwise format, allows sp|P26894|IL8_PIG INTERLEUKIN-8 PRECURSOR (IL-8) (ALVEOLAR ... 92 6e-21 gb|AAD02808| (AF061521) interleukin-8 [Bos taurus] 65 1e-12 one to easily visualize patterns of sp|P22952|AMC2_PIG ALVEOLAR MACROPHAGE CHEMOTACTIC FACTOR I... 58 2e-10 residue conservation in sequence sp|P80221|GCP2_BOVIN GRANULOCYTE CHEMOTACTIC PROTEIN 2 (GCP... 57 3e-10 families. sp|P30034|PLF4_PIG PLATELET FACTOR 4 (PF-4) 53 4e-09 sp|O46677|GROB_BOVIN GROWTH REGULATED PROTEIN HOMOLOG BETA ... 53 5e-09 As an example, consider the CxC sp|O46676|GROA_BOVIN GROWTH REGULATED PROTEIN HOMOLOG ALPHA... 53 5e-09 family of small cytokines. This sp|O46675|GROG_BOVIN GROWTH REGULATED PROTEIN HOMOLOG GAMMA... 52 7e-09 protein family is characterized by sp|P43030|PF4L_PIG PLATELET BASIC PROTEIN PRECURSOR (PBP) >... 52 7e-09 a conservation of four cysteine gi|2735499 (U95814) GRO [Ovis aries] 52 9e-09 residues involved in disulfide bond bbs|140204 neutrophil-activating peptide 2, pNAP-2-S {short... 51 2e-08 formation. One can compare the bbs|140202 neutrophil-activating peptide 2, pNAP-2-L {long... 51 2e-08 sp|P30035|PLF4_SHEEP PLATELET FACTOR 4 (PF-4) 49 8e-08 human sequence of Interleukin-8 pdb|1PLF|A Bos taurus >gi|494447|pdb|1PLF|B Bos taurus >gi|... 46 5e-07 (P10145), a member of this group, sp|P02777|PLF4_BOVIN PLATELET FACTOR 4 (PF-4) >gi|72110|pir... 44 3e-06 with the sequences of related bbs|161256 epithelial-derived neutrophil-activating peptide... 43 6e-06 cytokines from the sheep, pig, and cow by running a blastp search of tmpseq_1 1 LRCQCIKTYSKPFHPKFIKELRVIESGPHCANTEIIVKLSDGRELCLDP 49 the nr database using a 49–amino 463254 32 ...... H.T...... E.S...... TN.K.V.... 80 acid stretch from P10145 contain- 1699354 32 ...... H.T...... E.S...... TN.N.V..N. 80 516197 32 ...... N.H.T...... E.S...... VN.K.V.... 80 ing all four cysteines as the query. 346456 32 ...... N.H.T...... E.S...... VN.K.V.... 80 It is possible to exclude other very 1235612 32 ...... N.H.T...... E.S...... VN.K.V.... 80 closely related human sequences 4106336 1 ...... E.S...... TN.N.V..N. 35 and focus on the sheep, pig, and 399030 50 ...M.LT.-TPGI...M.SD.Q..PA..Q.SKA.V.AT.KN.K.V.... 97 cow by entering “Cetartiodactyla” 462169 10 ...V.LT.-TPGI...TVSD.Q..AA..Q.SKV.V.AT.KN...V.... 57 into the organism filter box on the 585702 23 ...V.V..I.G-VS..H.SS.E..GA....PSPQL.AT.KK.HKI.... 70 3913773 38 .....LQ.L-QGI.L.N.QSVK.TTP....DQ..V.AS.KT.Q.V..N. 85 BLAST search page. 3913772 38 .....LQ.L-QGI.L.N.QSVK.TTP....DQ..V.AS.KT.Q.V..N. 85 The search shown here was run 3913771 37 .....LQ.L-QGI.L.N.QSVK.TTP....DQ..V.AT.KT.Q.V..N. 84 using an Expect value of “.01,” 457754 52 ...L.LN.V.G-I..SN.QS.E..RA.A...KV.V.AT.KNDKKI.... 99 2735499 37 .....LQ.V-QGI.L.NMQSVK.TPP....GQ..V.AT.KT.Q.V..N. 84 and the Flat-Master Slave with 452976 6 ...L.LN.V.G-I..SN.QS.E..RA.A...KV.V.AT.KNDDKI.... 53 Identities alignment format. This 739009 13 ...L.LN.V.G-I..SN.QS.E..RA.A...KV.V.AT.KNDDKI.... 60 alignment format uses periods in 266800 23 .Q.V.L..T.G-I..RH.SS.E..GA.L..PSPQL.AT.KT..KI... 69 place of residues in the “slave” 494448 10 .Q.V.L..T.G-IN.RH.SS.E..GA.L..PSPQL.AT.KT..KI... 56 sequences (database hits) that are 225004 23 .Q.V.L..T.G-IN.RH.SS.E..GA.T..PSPQLLATKKT..KI... 69 identical to the aligned residues 861479 5 ...V.LT.-TPGI...TVSD.Q..AA..Q.SKV.V.AT.KN. 45 in the “master” sequence (the query sequence). The output here The BLAST Lab feature is intended to provide detailed technical infor- clearly shows the four conserved mation on some of the more specialized uses of the BLAST family of cysteine residues as uninterrupted programs. Topics are selected from the range of questions received by columns of periods (highlighted). the BLAST Help Group. — DW

6 Fall1999 NCBI News Q&A Frequently AskedQuestions

Q. A.

Is it possible to constrain a BLAST This is easily accomplished by using the organism filter box located in the search to a particular taxonomic middle of the Advanced BLAST page. Typing “mammalia” into this box will group, such as mammalia? limit your BLAST search to the taxon Mammalia. To browse the NCBI taxo- nomic tree in order to determine which taxon to use, follow the link below the organism filter box entitledExplore the taxonomy database at NCBI.

RefSeq NM_xxxxxx and GenBank No, both records will continue to be available. RefSeq and GenBank are AFxxxxxx appear to be duplicates. separate databases, and both are included in the Entrez Nucleotides data set. Will one be removed? RefSeq is a curated database in which each record encapsulates our current understanding of a gene, similar to a review article. In contrast, GenBank is an archival database where each record represents the work of a specific research group.

What is a taxonomy ID number The tax ID is a stable unique identifier for each taxon (for a species, a family, (tax ID)? an order, or any other group in the taxonomy database). The tax ID apppears in the GenBank records as a “source” feature, e.g., /db_xref=“taxon: 9606” for Homo sapiens.Tax IDs can be used to retrieve sequences in Entrez with a syntax such as: txid9606[organism].

This will retrieve only Homo sapienssequences. BLAST searches can also be limited to particular taxa by entering the tax ID into the organism filtering box.

How do I add a feature to my Once you have imported your sequence, use Sequin’s Annotatemenu to see sequence submission using the list of standard features. Select the feature of interest from the submenus, Sequin? for example, Coding Regions and Transcripts/CDS.This will invoke a feature-specific form that allows you to enter essential information about the feature and add it to your GenBank submission. To edit an existing feature, just double click on the feature. This will bring up a feature-specific form showing the current data, which can then be changed.

I have pasted a long sequence into No, you can specify a nucleotide range using the “From” and “To” boxes ORF-Finder, but only want ORFs below the query box. ORF-Finder will find ORFs only within the range within a small block. Should I specified. remove the surrounding sequence?

7 Fall1999 NCBI News New NCBI Home Page Site Maplink. The Site Map con- Electronic PCR, ORF Finder, Continued from page 1 tains an alphabetical listing of and other analysis software. The all services in tabular form, brief Educationlink leads to online descriptions of each, and an tutorials, sample exercises, A left-hand panel of links serves as expanded table of contents. overview articles, and other a table of contents for the entire teaching resources. site, grouping services into nine Take some time to explore. Under functional categories: About NCBI, About NCBI,you will find our The general organization of the GenBank, Molecular Databases, conference exhibit schedule and new home page has also been Literature Databases, Genomic NCBI News online. The GenBank extended to most of the other Biology, Tools, Research, Educa- page includes a sample record in NCBI pages in the site hierarchy, tion, and FTP Site. The central por- the database overview. The Molec- allowing for fluid navigation tion of the page offers illustrated ular Databasespage groups among related resources. and frequently updated information the sequence, mapping, structure, — BR, DW about new services and topics in the and taxonomy databases built news. A right-hand column of Hot from direct submissions. Genomic Spots highlights additional selected Biology pulls together resources resources. for compiling and analyzing gen- omic-scale data, such as UniGene, For a comprehensive, at-a-glance GeneMap ’99, RefSeq, and COGs. view of NCBI resources, follow the Under Tools,you will find BLAST,

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NCBINews NATIONAL INSTITUTES OF HEALTH • National Library of Medicine Fall 1999