Library Guides: Bioinformatics: Databases

Protein Databases

UniProt
According to their website, "[t]he mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information." Great for comparative searches. Includes useful add-ons, like automatic classification via TrEMBL.
BRENDA
A very comprehensive enzyme database, with searches by enzyme for anything from how to purify to its pH stability to its subunits, cofactors, substrates, organisms and applications.
CluSTr
From their website, "CluSTr database offers an automatic classification of UniProt Knowledgebase and IPI proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. "
InterProScan Sequence Search
Searches against sequences annotated in InterPro.
PRIDE
"Public repository for protein and peptide identifications together with the evidence supporting these identifications. PRIDE is also able to capture details of post-translational modifications coordinated relative to the peptides in which they have been found...[users can search with] protein accessions from IPI, UniProtKB, ENSEMBL or RefSeq, and you can also use UniProtKB IDs and NCBI gi numbers." (www.ebi.ac.uk/pride/)

Genomic Databases

Genome Review
According to their website, Genome Review "provides an up-to-date, standardised and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes...[and] is available as a MySQL relational database, or a flat file format derived from that in the EMBL Nucleotide Sequence Database."
Genome Expression Atlas
GEA is a search engine designed for, according to their website, "servicing queries for condition-specific gene expression patterns." Complete with conditions like search by organism, part of organism, disease factor, and others.
KEGG - Kyoto Encyclopedia of Genes and Genomes
Besides genes and genomes, it includes information about pathways, drugs, diseases, glycans, reactions, etc.

Article Databases

PubMed
An extensive medical publication database. Contains over 20 million citations!
CiteXplore
Uses text mining tools to extract cross-reference articles PubMed with applications (including many useful tools) from the EBI.
BioModels Database
According to their website, "BioModels Database is a repository of peer-reviewed, published, computational models. These mathematical models are primarily from the field of systems biology, but more generally are those of biological interest. This resource allows biologists to store, search and retrieve published mathematical models."

Computer Science Databases

Academic Search Complete
Academic Search Complete, designed specifically for academic institutions, is the world's most valuable and comprehensive scholarly, multi-disciplinary full-text database, with more than 8,700 full-text periodicals, including 4,400 peer-reviewed journals. In addition to full text, this database offers indexing and abstracts for more than 13,000 journals. The database features PDF content going back as far back as 1887.

Need help searching this database?
Use this tutorial.
http://support.epnet.com/training/flash_videos/adv_guided/EN_ehost_AdvSrch_Guided_Tut.ppt
ACM (Association for Computing Machinery) Digital Library
A half century of pioneering concepts and fundamental research have been digitized and indexed in a variety of ways in this special collection of works published by ACM since its inception. The ACM Digital Library includes bibliographic information, abstracts, but no full-text articles. Articles not available in the UNO Library can be ordered through Interlibrary Loan.
CiteSeerX
CiteSeerX is a scientific literature digital library and search engine that focuses primarily on the literature in computer and information science. CiteSeerX aims to improve the dissemination of scientific literature and to provide improvements in functionality, usability, availability, cost, comprehensiveness, efficiency, and timeliness in the access of scientific and scholarly knowledge.
Ebook Central by ProQuest
The Library provides access to over 200 electronic books from Ebrary, covering a variety of disciplines
Google Scholar
Google Scholar provides a simple way to broadly search for scholarly literature.
IEEE/IEL
This database allows you to search information about thousands of journal articles, conference proceedings, and more published by IEEE. Items can be requested through Interlibrary Loan.
Ingenta
This database allows searching of tables of contents of over 25,000 titles, with full-text provided for selected publications. Emphasis is on sciences and social sciences. The library has online access to the journal titles that it subscribes in print.
Springer LINK (Springer Verlag)
Link provides electronic access to Springer Verlag's journals. The UNO Library subscribes to 19 of these journals. This collection includes journals in the fields of Mathematics and the Sciences.
Science & Technology Collection
The Science & Technology Collection contains over 820 leading full text journals covering relevant aspects of the scientific and technical community. Topics include aeronautics, astrophysics, chemistry, computer technology, geology, aviation, physics, archaeology, and materials science. In addition to the full text, this database offers indexing and abstracts for more than 1,740 publications.
Synthesis Digital Library
This source provides 50-100 page "lectures"; self-contained electronic books that synthesize an important research or development topic in engineering or computer science and authored by an expert in the field.
WorldCat
This combined catalog of library holdings includes books, web resources, and other material. A search for a title will show which participating libraries own it.