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Systems Biology

This page features library resources for programs in the School of Systems Biology

NCBI: National Center for Biotechnology

NCBI: Tools for data mining The gateway to the data mining tools offered at the National Center for Biotechnology(NCBI). Includes the tools for nucleotide sequence analysis, protein sequence analysis and proteomics, structures, genome analysis, gene expression, and programming.

  • Search NCBI  Integrated, text-based search and retrieval system used at National Center for Biotechnology Information for the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others. Formerly Entrez.
  • Genome Workbench  An integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix these data with your own data.

  • Genome Data Viewer The NCBI Genome Data Viewer (GDV) is a genome browser supporting the exploration and analysis of eukaryotic RefSeq genome assemblies. It allows users to visualize different types of sequence-associated data in a genomic context. (Replacement for Map Viewer)

  • ProSplign A utility for computing alignment of proteins to genomic nucleotide sequence. It is based on a variation of the Needleman Wunsch global alignment algorithm and specifically accounts for introns and splice signals. Due to this algorithm, ProSplign is accurate in determining splice sites and tolerant to sequencing errors.

  • BLAST Link (BLink) A link option on protein records that displays the results of a pre-computed BLAST search of that protein against all other protein sequences at NCBI.

Data repositories

  • Protein Data Bank Includes three-dimensional structural data of large biological molecules, such as proteins and nucleic acids.