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Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new datasets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors, and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers. Sequenceserver is AGPLv3-licensed at https://sequenceserver.com.
This article was published in the following journal.
Name: Molecular biology and evolution
A new version of FoldX, whose main new features allows running classic FoldX commands on structures containing RNA molecules and includes a module that allows parametrization of ligands or small molec...
The Java software jBar consists of a graphical user interface that allows the user to customize and assemble an included script for R. The scripted R pipeline calculates means and standard errors/devi...
Creating input files to atomistic simulations and quantum chemical calculations in the CP2K software package can be a challenge. Here, we present a new graphical user interface to reduce the complexit...
Optimization of coding sequences to maximize protein expression yield is often outsourced to external service providers during oligonucleotide synthesis and thus remains a black box for many researche...
Nowadays, bioinformatics is one of the most important areas in modern biology and the creation of high-quality scientific software supporting this recent research area is one of the core activities of...
The purpose of this study is to validate the user interface of TOBI Podhaler by establishing that the product can support safe and effective use for the intended users
This study is designed to evaluate the information provided to the clinicians by the surgical imaging device. It is also to gain insight on the user interface and how "user friendly" it is...
This study will conduct a preliminary evaluation of and obtain user data on a novel game-based visual interface for stroke gait training. Study participants will complete one session compr...
Memory and cognitive declines are associated with normal brain aging but are also precursors to dementia, in particular the so called the pandemic of the century, Alzheimer's disease. Whil...
Non-invasive ventilation (NIV) is an important therapy for patients with a number of neurological diseases. Specifically, NIV has been shown to be an effective treatment for people with am...
The portion of an interactive computer program that issues messages to and receives commands from a user.
A microcomputer-based software package providing a user-friendly interface to the MEDLARS system of the National Library of Medicine.
Databases devoted to knowledge about specific chemicals.
Databases devoted to knowledge about specific genes and gene products.
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
Biological therapy involves the use of living organisms, substances derived from living organisms, or laboratory-produced versions of such substances to treat disease. Some biological therapies for cancer use vaccines or bacteria to stimulate the body&rs...