Biological Research Databases & Software

Protein Databases

UniProt

uniprot.org

The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

PaxDb

pax-db.org

PaxDB is a comprehensive absolute protein abundance database, which contains whole genome protein abundance information across organisms and tissues.

BioGPS

biogps.org

BioGPS is a gene portal built with two guiding principles in mind -- customizability and extensibility.

CiteAb

citeab.com

CiteAb’s antibody and biochemical search engine provides a simple way for researchers to find reagents that work.

NCBI

ncbi.nlm.nih.gov

The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.

InterPro

ebi.ac.uk/interpro

InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.

The Human protein Atlas

proteinatlas.org

The Human Protein Atlas arims to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology.

ExPASy

expasy.org

ExPASy is an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences.

UniHI

unihi.org

Users can enter gene or protein identifiers from different organisms to obtain physical and regulatory interaction partners in the human interactome.

Protein Data Bank

wwpdb.org

Since 1971, the Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

BioGRID

thebiogrid.org

BioGRID is an interaction repository with data compiled through comprehensive curation efforts. The index searches publications for protein and genetic interactions, chemical associations and post translational modifications from major model organism species.

PIR

pir.georgetown.edu

The Protein Information Resource (PIR) is an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies.

BRENDA - Enzyme Database

brenda-enzymes.org

BRENDA is the main collection of enzyme functional data available to the scientific community.

CORUM

mips.helmholtz-muenchen.de/corum

Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM database is a collection of experimentally verified mammalian protein complexes.

IUPHAR/BPS Guide to PHARMACOLOGY

guidetopharmacology.org

This website is intended to become a “one-stop shop” portal to pharmacological information. The searchable database provides quantitative information on drug targets and the prescription medicines and experimental drugs that act on them. It aims to offer accurate information on the basic science underlying drug action.

LOCATE

locate.imb.uq.edu.au

LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set.

Bioscience Research Protocol Resources

JoVE

jove.com

JoVE creates the ultimate solutions for advancing research and science education by making and publishing videos of scientific experiments from the top laboratories around the globe.

Cold Spring Harbor Protocols

cshprotocols.cshlp.org

Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging.

Bio-101

bio-protocol.org/bio101/Default.aspx

Bio-101 is an online database of life science protocols. Its mission is to make life science research more efficient and reproducible by curating and hosting high-quality, experimentally validated, freely accessible protocols.

Protocol Online

protocol-online.org

Protocol Online is a database of research protocols in a variety of life science fields. It contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites.

Data Processing & Analysis Software

Sigma Plot

systatsoftware.com/products/sigmaplot

SigmaPlot is a software package for scientific graphing and statistical data analysis.

SPSS

ibm.com/analytics/spss-statistics-software

The IBM SPSS® software platform offers advanced statistical analysis, a vast library of machine-learning algorithms, text analysis, open-source extensibility, integration with big data and seamless deployment into applications.

Origin

originlab.com

Origin is an industry-leading scientific graphing and data analysis software.

Office Excel

products.office.com/en/excel

Microsoft Excel is the industry leading spreadsheet program, a powerful data visualization and analysis tool.

Statistica

community.tibco.com/products/tibco-statistica

TIBCO Statistica advanced analytics and data science platform helps you to embed analytics everywhere, empower more people and innovate faster.

SigmaStat

systatsoftware.com/products/sigmastat

SigmaStat provides a wide range of powerful yet easy-to-use statistical analyses designed to meet the needs of research scientists and engineers.

Photo Editing Software

Adobe Illustrator

adobe.com/products/illustrator.html

Adobe Illustrator is a vector graphics editor developed and marketed by Adobe Inc.

ChemSketch

acdlabs.com/resources/freeware/chemsketch

ACD/ChemSketch Freeware is a drawing package that allows you to draw chemical structures including organics, organometallics, polymers, and Markush structures. It also includes features such as calculation of molecular properties (e.g., molecular weight, density, molar refractivity etc.), 2D and 3D structure cleaning and viewing, functionality for naming structures (fewer than 50 atoms and 3 rings), and prediction of logP.

Photoshop

adobe.com/products/photoshop.html

Adobe Photoshop is an imaging and graphic design software developed and published by Adobe Inc. for macOS and Windows.

Image Pro Plus

mediacy.com/imageproplus

Image-Pro Plus image analysis software makes it easy to acquire images, count, measure and classify objects, and automate your work.

Edraw Max

edrawsoft.com

Edraw Max is a 2D business technical diagramming software which helps create flowcharts, organizational charts, mind map, network diagrams, floor plans, workflow diagrams, business charts, and engineering diagrams.

Scientific Literature Resources

NCBI

ncbi.nlm.nih.gov

The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.

PubMed

ncbi.nlm.nih.gov/pubmed

PubMed comprises more than 29 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

DOAJ (Directory of Open Access Journals)

doaj.org

DOAJ is a community-curated online directory that indexes and provides access to high quality, open access, peer-reviewed journals.

Research Paper Management Tools

EndNote

endnote.com

EndNote is a reference management software that not only frees you from the tedious work of manually collecting and curating your research materials and formatting bibliographies, but also gives you greater ease and control in coordinating with your colleagues.

Mendeley

mendeley.com

Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research.

NoteExpress

inoteexpress.com/index.htm

NoteExpress is designed to help you organize research notes and bibliographic references, generate bibliographies automatically, and search and capture bibliographic data from Internet with efficiency and ease.

Molecular Biology Software

Vector NTI

thermofisher.com/vector-nti-software.html

Vector NTI software is a completely integrated suite of sequence analysis and design tools that help you manage, view, analyze, transform, share, and publish diverse types of molecular biology data, all within one graphically rich analysis environment.

DNAMAN

lynnon.com

DNAMAN is a one-for-all software package for molecular biology applications. This package can perform restriction analyses, multiple sequence alignment, PCR primer design, protein sequence analysis, and plasmid drawing.

DNAStar

dnastar.com/software/molecular-biology

DNASTAR’s Molecular Biology Suite is a comprehensive sequence analysis and alignment software for molecular biology research. The suite provides software solutions for DNA, RNA and protein editing and annotation, Sanger sequence assembly, multiple sequence alignment, virtual cloning, primer design and comprehensive sequence analysis.

SnapGene

snapgene.com

SnapGene offers a fast and easy way to plan, visualize, and document your everyday molecular biology procedures.

Primer Design Tools

Primer Premier

premierbiosoft.com/primerdesign

Primer Premier's search algorithm finds optimal PCR, multiplex and SNP genotyping primers with the most accurate melting temperature using the nearest neighbor algorithm.

NCBI - Primer-BLAST

ncbi.nlm.nih.gov/tools/primer-blast

NCBI’s Primer-BLAST tool is for designing PCR primers and checking them for specificity.

Oligo

oligo.net

OLIGO Primer Analysis Software is the essential tool for designing and analyzing sequencing and PCR primers, synthetic genes, and various kinds of probes including siRNA and molecular beacons.

Array Designer

premierbiosoft.com/dnamicroarray

Array Designer is a microarray software that enables fast, efficient design of specific oligos for making whole genome arrays, tiling arrays and resequencing arrays.

Bioinformatics Tools

Programming Languages

Python

python.org

Python is a programming language that lets you work quickly and integrate systems more effectively.

Biopython

biopython.org

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.

Perl

perl.org

Perl 5 is a highly capable, feature-rich programming language with over 30 years of development.

BioPerl

bioperl.org

The Bioperl Project is an international association of users & developers of open source Perl tools for bioinformatics, genomics and life science.

Java

java.com

Java is a general-purpose computer-programming language that is concurrent, class-based, object-oriented, and specifically designed to have as few implementation dependencies as possible.

BioJava

biojava.org

The open-source Java framework for bioinformatics.

Software

FastQC

bioinformatics.babraham.ac.uk/projects/fastqc

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

Bwa

bio-bwa.sourceforge.net

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.

Samtools

htslib.org

Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories - Samtools, BCFtools, HTSlib.

Bowtie 2

bowtie-bio.sourceforge.net/bowtie2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Bedtools

bedtools.readthedocs.io

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.

Frequently used websites

OMICtools

omictools.com

omicX is a global benchmark in big biodata analytics. Powered by machine teaching, its unique dynamic analytics ecosystem deciphers and analyses life science data.

Ensembl

ensembl.org

The Ensembl project started in 1999 with the goal to automatically annotate the human genome, integrate this annotation with other available biological data, and make all this publicly available via the web. Since then, many more genomes have been added to Ensembl and the range of available data has expanded to include comparative genomics, variation and regulatory data.

UCSC Genome Browser

genome.ucsc.edu

The UCSC Genome Browser provides a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data.

ENCODE

encodeproject.org

The Encyclopedia of DNA Elements (ENCODE) is a public research project which aims to identify functional elements in the human and mouse genomes.

Phylogenetic Tree Analysis

Mega

megasoftware.net

MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.

TREE-PUZZLE

tree-puzzle.de

TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.

FigTree

tree.bio.ed.ac.uk/software/figtree

FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.

DNASTAR - MegAlign

dnastar.com/software/molecular-biology

MegAlign is DNASTAR’s software application providing both DNA and protein sequence alignment using a range of pairwise sequence alignment and multiple alignment methods. Use bootstrapping to test for consistency and robustness of phylogenetic trees created using one of the Clustal methods.

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