NCBI News National Center for Biotechnology Information National Library of Medicine National Institutes of Health Winter 2000 New Entrez Genomes Views: Links to the Mitelman summary of chromosome aberrations assoc- A Fresh Look at Human Chromosomes iated with cancers. A set of new Entrez Genomes display For each chromosome, the new A selection of disease genes that formats provides an improved van- Entrez Genomes views now provide: map to the chromosome:Links tage point on the human chromo- are also given to the Genes and somal sequences in GenBank, facili- A graphic depicting sequencing Disease Web site, OMIM, and tating convenient access to finished progress with finished regions OMIM Morbid Map. contig data and more supplementary shown in red: Clicking on a finished information than ever before. Figure region leads to the corresponding Links to references giving infor- 1 shows a partial Entrez Genomes contig data. mation on the chromosomal view of human chromosome 22, sequence: For example, the Entrez illustrating many of the features Sequencing progress statistics: Genomes view for chromosome 22 highlighted here. These include euchromatic size, gives a link to the full text of the amount of finished paper by Dunham et al. (Nature sequence given (1999) 402, 489-95) that reports in kilobases or as the completion of chromosome 22 a percentage of the sequencing. chromosome, and the number of con- To see the human chromosome tigs available for views, go to www.ncbi.nlm.nih.gov/ the chromosome. genome/guide.— RM, DW Links to contig lists sorted by size and In this issue position. 1 Entrez Genomes Links to various 2 IgBLAST STS maps. 2 BLAST1.4 3 PubMed Central Links to the coor- 4 News Briefs dinating chromo- 4 Mitochondria Energize RefSeq some sequencing 4 PSI-BLAST Profiles center: Other 5 Frequently Asked Questions sequencing centers 6 Textbooks Linked to PubMed that are working 6 BankIt 3.0 on thechromosome are listedas well. 6 Mouse and Rat in LocusLink 7 BLASTLab Figure 1: Entrez Genomes View of Human Chromosome 22. [Reprinted by permission from Nature402(6761):489-95, copyright 8 Malaria Menace Mapped 1999Macmillan Magazines Ltd.] IgBLAST: NCBINews An Immunoglobulin-Specific Search Tool Immunoglobulin BLAST (IgBLAST), by the best hits to the nr database. a specialized variant of BLAST One additional feature of IgBLAST NCBI Newsis distributed four times a year. We welcome communication that is designed for the analysis of is its ability to flag the returned from users of NCBI databases and human or mouse immunoglobulin matches from the nr database software and invite suggestions for sequence data, is now available on- according to their germline V-gene articles in future issues. Send corre- line from NCBI. IgBLAST performs origins. This allows one to distin- spondence to NCBI News at the address below. blastn or blastp searches of a non- guish easily between the results NCBI News redundant (nr) database of germline that use the same germline V-gene National Library of Medicine V genes and returns the best three as the query and those that do not. Bldg. 38A, Room 8N-803 V-gene matches, and the best two D- 8600 Rockville Pike gene and J-gene matches. IgBLAST Although IgBLAST also supports Bethesda, MD 20894 Phone: (301) 496-2475 also annotates the query sequence, protein searches using blastp, only Fax: (301) 480-9241 based on the domain information V-gene matches will be reported. E-mail: [email protected] drawn from an alignment between D-gene and J-gene matches are Editors the top-matched germline V gene reported only for DNA searches Dennis Benson and the query sequence, using the with blastn. Barbara Rapp nomenclature of the Kabat Data- Contributors base of Sequences of Proteins of The germline V-gene database Renata McCarthy Jo McEntyre Immunological Interest. Such fea- currently contains Igh, Ig kappa, Ig Margaret McGhee tures as framework regions (FWR1, lambda, and D and J genes from Liz Pope for instance) or complementarity- both human and mouse. The data- Jian Ye determining regions (CDR1, for base can be viewed in the form of Writer instance) are delineated. an annotated multiple sequence David Wheeler alignment by clicking on the appro- Editing, Graphics, and Production IgBLAST may also be used to search priate database link in the sidebar Marla Fogelman Veronica Johnson the standard BLAST nr database. In of the IgBLAST page. Jennifer Vyskocil this case, the best matches to the Design Consultant germline gene database are aligned Try IgBLAST at www.ncbi.nlm.nih. Gary Mosteller with the query as before, followed gov/igblast.— DW, JY In 1988, Congress established the National Center for Biotechnology Information as part of the National Old BLAST 1.4 Network Server Retired Library of Medicine; its charge is to create information systems for The old BLAST 1.4 network server, Blast outside of Sequin. Blastcl3, molecular biology and genetics which accounts for less than 3% of available at ftp://ncbi.nlm.nih.gov/ data and perform research in computational molecular biology. all BLAST jobs performed at NCBI, blast/network/netblast, should be The contents of this newsletter may was retired on March 1, 2000. It was used instead. MacVector versions be reprinted without permission. replaced by BLAST 2.0, which was prior to 6.5.3 are also affected by The mention of trade names, com- designed to handle the increasing this change. mercial products, or organizations size and complexity of the sequence does not imply endorsement by NCBI, NIH, or the U.S. Government. databases. This change will notaffect the NCBI BLAST Web pages, e-mail server, NIH Publication No. 00-3272 The following NCBI programs used GCG connection, blastcl3 client, ISSN 1060-8788 ISSN 1098-8408 (Online Version) BLAST 1.4 and will no longer func- PowerBlast within Sequin, or Mac- tion: blastcl2, blastcli, and Power- Vector at release 6.5.3 and higher. Winter 2000 NCBI News 2 PubMed Central Archive Developed Selected Recent at NCBI Publications by PubMed Central is a Web-based presentation, and navigation; and NCBI Staff repository established at the archiving the content to guarantee National Institutes of Health (NIH) accessibility in the future. Boguski, MS.Biosequence exegesis. to provide barrier-free access to Science286(5439):453–5, 1999. primary research reports in the life How to Access Gerlach, VI, L Aravind,G Gotway, sciences. So named because of its RA Schultz, EV Koonin,and EC natural integration with the existing PubMed Central began accepting Friedberg. Human and mouse homo- research reports this year and logs of Escherichia coliDinB (DNA PubMed retrieval system, PubMed polymerase IV), members of the Central will serve as a host for is now accessible on the Web at UmuC/ DinB superfamily. Proc Natl scientific publishers, professional www.pubmedcentral.nih.gov. Acad Sci USA 96(21):11922–7, 1999. societies, and other groups to Grishin, NV.Phosphatidylinositol From the home page, select a title archive, organize, and distribute phosphate kinase: a link between pro- to see the table of contents of the their research articles at no cost to tein kinase and glutathione synthase most recent issue available. From folds. J Mol Biol291(2):239–47, 1999. the user. there, select specific articles or Koonin, EV, L Aravind,K Hofmann, click on the Archivebox for back J Tschopp, and VM Dixit. Apoptosis. Content issues. Enhanced search capabili- Searching for FLASH domains. Nature401(6754):662–3, 1999. The scope of PubMed Central in- ties are currently under develop- cludes the broad life sciences, en- ment. Links to publishers’ sites are Panchenko, A, A Marchler-Bauer, compassing plant and agricultural also included. andSH Bryant.Threading with explicit models for evolutionary con- research as well as biology and servation of structure and sequence. medicine. Participating journals Two journals,Molecular Biology Proteins Suppl 3:133–40, 1999. and editorial groups may submit of the Celland PNAS: The Pro- Spouge, JL, A Marchler-Bauer, and ceedings of the National Academy peer-reviewed reports from jour- S Bryant.The combinatorics and ex- nals, as well as screened, although of Sciencesare currently available. treme value statistics of protein thread- not formally peer-reviewed, reports Journals currently in process in- ing. Ann Combinatorics3:81–93, 1999. from recognized editorial boards. clude Biochemical Journal, Su, X, MT Ferdig, Y Huang, CQ Huynh, Canadian Medical Association A Liu, J You, JC Wootton,and TE Wellems. A genetic map and recombi- Participants’ Roles Journal, Frontiers in Bioscience, and five journals from BioMed nation parameters of the human malar- Contributing publishers, societies, ia parasite Plasmodium falciparum. Central. Many additional journals Science286(5443):1351–3, 1999. and other editorial groups inde- have expressed interest and are Tatusova, TA, I Karsch-Mizrachi, pendent of the NIH have complete preparing content for submission. andJA Ostell.Complete genomes responsibility for their input. An in WWW Entrez: data representation international PubMed Central How to Participate and analysis. Bioinformatics15(7): advisory committee establishes 536–43, 1999. Guidelines covering acceptance criteria for certifying groups that Wheelan, SJ, MS Boguski, L Duret, may submit material. criteria, media formats, copyright, andW Makalowski.Human and and data formats are available nematode orthologs—lessons from NIH’s responsibilities, to be carried from the PubMed Central home the analysis of 1,800 human genes and the proteome of the Caenorhabditis out by NCBI, pertain to developing, page under theAbout PubMed elegans. Gene238(1):163–70, 1999. maintaining, and providing access Centrallink. to the repository. This includes Wolfsberg, T,and I Makolowska. Web alert. Pattern formation and dev- facilitating the submission of SGML- Organizations interested in depos- elopmental mechanisms. Curr Opin tagged content;developing tech- iting content are urged to contact us Genet Dev 9(4):385–6, 1999.