GenBank and NCBI Resources
National Center for Biotechnology Information
National Library of Medicine
National Institutes of Health
July 4th, 2000
David Landsman
NCBI, NLM, NIH

 email:
phone:

 		landsman@ncbi.nlm.nih.gov
301-435-5981
Online resources:
Slides:

Problem Set: 		http://www.ncbi.nlm.nih.gov/Class/FieldGuide/Slides/

http://www.ncbi.nlm.nih.gov/Class/FieldGuide/problem_set.html
                                                                                                                                                                                       


General:
NCBI Homepage: http://www.ncbi.nlm.nih.gov
Site Map: http://www.ncbi.nlm.nih.gov/Sitemap/index.html
NCBI News: http://www.ncbi.nlm.nih.gov/About/newsletter.html
NCBI Education page http://www.ncbi.nlm.nih.gov/Education/index.html


GenBank:
GenBank Release Notes: ftp://ncbi.nlm.nih.gov/genbank/gbrel.txt
dbEST: http://www.ncbi.nlm.nih.gov/dbEST/index.html
dbSTS: http://www.ncbi.nlm.nih.gov/dbSTS/index.html
dbGSS: http://www.ncbi.nlm.nih.gov/dbGSS/index.html


Entrez:
Entrez: http://www.ncbi.nlm.nih.gov/Entrez/
Batch Entrez for creating custom databases: http://www.ncbi.nlm.nih.gov/Entrez/batch.html
Network Entrez: ftp://ncbi.nlm.nih.gov/entrez/CURRENT/


BLAST:
BLAST Main Page: http://www.ncbi.nlm.nih.gov/BLAST/
Stephen Altschul’s Lectures on BLAST statistics: http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html
Frequently Asked Questions: http://www.ncbi.nlm.nih.gov/BLAST/blast_FAQs.html
Online BLAST tutorial: http://www.ncbi.nlm.nih.gov/Education/blasttutorial.html
BLAST Clients, Executables and Databases:  ftp://ncbi.nlm.nih.gov/blast/
NCBI Source Code: ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools/


NCBI Structures:
Structure Homepage: http://www.ncbi.nlm.nih.gov/Structure/
Cn3D tutorial: http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dtut.html


Genomic Resources:
Entrez Genomes: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome
Human Genome Resources: http://www.ncbi.nlm.nih.gov/genome/guide
LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/
UniGene: http://www.ncbi.nlm.nih.gov/UniGene/
Human Genome Sequencing: http://www.ncbi.nlm.nih.gov/genome/seq/
CGAP: http://www.ncbi.nlm.nih.gov/ncicgap/


Email addresses:
    Humans:
    General Help
info@ncbi.nlm.nih.gov
    Updates
update@ncbi.nlm.nih.gov
    BLAST
blast-help@ncbi.nlm.nih.gov
    Sequin Submissions
gb-sub@ncbi.nlm.nih.gov
    Batch Submissions
batch-sub@ncbi.nlm.nih.gov
    Servers:
    BLAST Server:
blast@ncbi.nlm.nih.gov
    Query Server:
query@ncbi.nlm.nih.gov


Literature Reference List
    General
    Baxevanis, A. and Ouellette, B.F.F., eds. 1998. Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. New York: John Wiley & Sons

    Wheeler DL,  et al. 2000. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 28(1):10-14. PMID: 10592169
    GenBank Database
    Benson DA,  et al. 2000. Genbank. Nucleic Acids Res. 28(1):15-18. PMID: 10592170
    BLAST
    Altschul SF, et al. 1990. Basic local alignment search tool.  J Mol Biol. 215(3):403-10. PMID: 2231712.
    Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17):3389-402.  PMID: 9254694.
    Altschul SF, et al. 1998. Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases.  Trends Biochem Sci. 23(11):444-7. PMID: 9852764.
    Tatusova TA, et al.  1999. BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences.  FEMS Microbiol Lett. 174(2):247-50.  PMID: 10339815.
    Zhang Z, et al. 1998. Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res. Sep 1;26(17):3986-90. PMID: 9705509.
    MMDB and Structures
    Hogue CW. 1997. Cn3D: a new generation of three-dimensional molecular structure viewer. Trends Biochem Sci. 22(8):314-6. PMID: 9270306.
    Marchler-Bauer A, et al. 1999. MMDB: Entrez's 3D structure database.

    Nucleic Acids Res. Jan 1;27(1):240-3. PMID: 9847190. Wang Y, et al. 2000. MMDB: 3D structure data in Entrez.Nucleic Acids Res. 28(1):243-245.PMID: 10592236
    Specialized Genomic Resources
    Deloukas P, et al. 1998.  A physical map of 30,000 human genes. Science. 82(5389):744-6. PMID: 9784132
    Jang W, et al. 1999.  Making effective use of human genomic sequence data. Trends Genet. 15(7):284-6.  PMID: 10390628.
    Smigielski EM, et al. 2000. dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res. 28(1):352-355. PMID: 10592272
    Tatusov RL, et al.  2000 The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28(1):33-6. PMID: 10592175