institute for computational biomedicine: NCBI Databases

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[ description ]

The ICB keeps a local copy of the amino acid and nucleotide databases available from NCBI.

[ documentation ]

The databases are downloaded from the NCBI ftp site. These databases are updated on the first day of every month. All amino acid databases are also filtered using the pfilt command. The databases that are kept locally are:

amino acid databases

Alu sequences: translated consensus sequences for Alu repeats

nr: non-redundant GenBank protein sequences

PDB: sequences of proteins with structures in the Protein Databank

swissprot: proteins available from SwissProt

nucleotide databases

Alu sequences: consensus sequences for Alu repeats

human ESTs: the human sequences from dbEST

mouse ESTs: the mouse sequences from dbEST

other ESTs: all other EST sequences from dbEST

nti: non-redundant GenBank nucleotide sequences

[ availability ]

NCBI databasesare available from all machines [ access NCBI databases]

News

Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]
Apr, 2009; The BDVal program developed by the Campagne laboratory for MAQC-II is now available from http://bdval.org. The software supports the development and evaluation of predictive biomarker models from high-throughput data. The web site offers binary and source distributions. [More]
Jan, 2009; Twease now supports searching MEDLINE articles by Author, Journal, and Publication Year. Examples for performing these searches can be found in the updated Twease tutorial. [More]

[News Archives] [Mailing List]

Events

Dec 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Fabien Campagne; ICB Conference Room - Y.1301
Jan 15th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Lei Shi; ICB Conference Room - Y.1301
Feb 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Christopher E. Mason; ICB Conference Room - Y.1301
Mar 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Olivier Elemento; ICB Conference Room - Y.1301
Apr 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Emre Aksay; ICB Conference Room - Y.1301
May 14th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Jonathan D. Victor; ICB Conference Room - Y.1301
Jun 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Harel Weinstein; ICB Conference Room - Y.1301
Jul 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Duane Hassane; ICB Conference Room - Y.1301