Skip to Content
ublogo print

University at Buffalo Libraries

Bioinformatics


Top Resources

Current Protocols Collection

Designed in consultation with bench scientists, the Current Protocols suite is a collection of standard research methods in the biosciences, divided into separate publications in various topical areas. UB Libraries subscribes to the following:

Current Protocols in Bioinformatics: Step-by-step instructions for working with bioinformatics databases, tools, software, and more.

Current Protocols in Cell Biology: Methods for analysis of the relationship between specific molecules and genes, and their locations, functions, and structure at the cellular level.

Current Protocols in Molecular Biology: Covers basic methods in nucleic acid isolation and purification, and protein expression, as well as advanced protocols relating to next-generation sequencing, microarrays, single cell analysis, PCR, gene silencing, and more.

Current Protocols in Nucleic Acid Chemistry: Covers basic to advanced techniques for the synthesis, modification, purification, protection, analysis, and utilization of nucleic acids, nucleotides, and nucleosides. Includes methods for analysis of structure-function, binding and cross-linking.

Current Protocols in Protein Science: Presents methods for studying and quantifying protein interactions, as well as many protocols for proteomics analyses and protein engineering.

  More Info

UB ONLY

Cold Spring Harbor Protocols

Monthly electronic journal detailing a mix of well-established and emerging research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging.   More Info

UB ONLY

Galaxy

Galaxy is a web-based front end to a suite of bioinformatics software and tools that permits researchers without any programming skills to build a multi-step, customized computational set of genomic pipeline analyses. Users can upload their own sequence, alignment, interval or tabular data, analyze it with their custom built Galaxy pipeline, then publish or share the results. Built-in file format converters are provided, including converting genome coordinates between assemblies and genomes. Analyses include sequence alignments, FASTA manipulations, various statistical manipulations, plotting tools to graph/display data, DAVID functional annotation, phenotype to sequence associations, RNA analysis and phylogenetic analysis, a set of ENCODE analysis options, and much more.

PUBLIC

Methods in Enzymology

A series of publications focused primarily on biochemistry that details methodology and related reagents, compares/contrasts various techniques, methods overviews and critical reviews, and protocol troubleshooting.

Full-Text
UB ONLY

Nature Methods

Nature Methods is a monthly scientific research journal dedicated to publishing high impact emerging methods and tools for laboratory researchers in the life sciences.   More Info

UB ONLY

Nature Protocols

Nature Protocols is an online journal of laboratory protocols for bench researchers. Protocols are presented in a 'recipe' style providing step-by-step descriptions of procedures which users can take to the lab and immediately apply in their own research. The journal selects those protocols that are used to answer outstanding contemporary questions in the life sciences that have practical application to the study of biological problems. This includes topical areas such as enzymology, NMR, thermodynamics, apoptosis, cell cycle, primary cell culture, stem cells, transfection, microarrays, management and analysis of sequence data, intron/exons, protein folding/unfolding, structure-activity relationships, statistics, next generation sequencing, molecular diagnostics, genomics, gene expression, electrophoresis, antibodies, MRI/PET/SPECT, biofilms, metagenomics, model organisms, nanotechnology, imaging, proteomics, drug metabolites and target identification, structural biology, synthetic biology, toxicology and virology.

Full-text from Volume 1, 2006

  More Info

UB ONLY

NCBI BLAST Suite

The Basic Local Alignment Search Tool (BLAST) is a combination statistical and mathematical equation created by the National Center for Biotechnology Information (NCBI). The BLAST Suite offers a set of tools for identifying areas of similarity between various kinds of genomic and protein sequences as well as specialized BLAST tools for Polymerase Chain Reaction (PCR), comparing sequences, identifying mutations, sequences binding molecules such as drugs, and more.   More Info

PUBLIC

NCBI Gene

The Gene database provides detailed information (transcripts, variations, proteins, domains, diseases, homologies, etc.) encoded by known and predicted genes. Each record in the database has its origins in a NCBI Reference Sequence and corresponds to a single gene from any given organism. In 2013, Gene contained close to 14.4 million entries from all major taxonomic groups. Each Gene record represents a "jump station" to continuously updated knowledge for any given gene by providing a contextual library of hyperlinks for each gene sequence that links to other NCBI resources, journal articles, and to peer-reviewed third party Internet databases.   More Info

PUBLIC

PubMed

PubMed comprises more than 23 million biomedical literature citations from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central, free full-text from Open Access, NCBI sequence databases, and publisher web sites for which the UB Libraries subscribes to full-text content.   More Info

PUBLIC

OMIM

Online Mendelian Inheritance in Man (OMIM®) is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression. It is considered to be a phenotypic companion to the Human Genome Project. OMIM is currently biocurated at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine. Although you may still search OMIM through NCBI (http://www.ncbi.nlm.nih.gov/omim), the regularly updated database and full range of search functions are now maintained at omim.org.   More Info

PUBLIC

PharmGKB

The PharmGKB is a pharmacogenomics knowledge resource that encompasses clinical information (including dosing guidelines and drug labels), potential clinically actionable gene-drug associations, and genotype-phenotype relationships. PharmGKB collects, curates and disseminates knowledge about the impact of human genetic variation on drug responses. To view and download clinical and variant data, users must register here.   More Info

PUBLIC

Springer Protocols

Springer Protocols contains in excess of 30,000 protocols and methodologies, most of which are derived from the book series Methods in Molecular Biology, published by Humana Press. You may search each book separately using the “Source Title List” hyperlink, or through individual articles organized into 15 subject categories, including cell biology, bioinformatics, imaging/radiology, infectious disease, pharmacology, genomics, cancer research, and more.   More Info

UB ONLY

UCSC Genome Browser for Animals

The UCSC Genome Browser permits researchers to rapidly browse a large number of vertebrate, invertebrate, microbial and model organism genomes. Any portion of any genome may be retrieved at any scale, together with dozens of aligned annotation tracks (known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, chromosomal bands, mouse homologies, and more). Users can also add their own custom tracks to the browser for educational or research purposes. In addition, the Browser provides portals to ENCODE data, the Neanderthal sequences, and is home to the popular sequence alignment tool, BLAT.

More info on the Browser or BLAT

PUBLIC

UCSC Genome Browser for Microbes

The UCSC Genome Browser for microbes is a subset dataset of the UCSC Genome browser which permits researchers to rapidly browse more than 300 microbial species from Bacteria and Archaea domains, including archaeal viral genomes. Based upon a slightly modified UCSC Genome Browser, information is presented tracks aligned along the microbial genome sequence which can be hidden, expanded and customized to display exactly what data and format is needed.

PUBLIC

News