GenBank and NCBI Resources

National Center for Biotechnology Information
National Library of Medicine
National Institutes of Health

David Landsman
NCBI, NLM, NIH
email:
phone: 301-435-5981

July 4th, 2000

Online resources:

• Slides: http://www.ncbi.nlm.nih.gov/Class/FieldGuide/Slides/
• Problem Set: https://wp.pongor2.itk.ppke.hu/tutorials/ncbi-problem-set/

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:
• Updates:
• BLAST:
• Sequin Submissions:
• Batch Submissions:

Servers:

• BLAST Server:
• Query Server:

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