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Tools used in Bioinformatics
BLAST
In Bioinformatics, BLAST (basic local alignment search tool) is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a query) with a library or database of sequences, and identify database sequences that resemble the query sequence above a certain threshold.
CLUSTAL OMEGA
Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. For the alignment of two sequences please instead use our pairwise sequence alignment tools.
CLUSTAL OMEGA
Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. For the alignment of two sequences please instead use our pairwise sequence alignment tools.
TBTOOLS
TBtools (a Toolkit for Biologists integrating various biological data-handling tools), a stand-alone software with a user-friendly interface. The toolkit incorporates over 130 functions, which are designed to meet the increasing demand for big-data analyses, ranging from bulk sequence processing to interactive data visualization. A wide variety of graphs can be prepared in TBtools using a new plotting engine (“JIGplot”) developed to maximize their interactive ability; this engine allows quick point-and-click modification of almost every graphic feature. TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer.
DNAMAN
DNAMAN is a one-for-all software package for molecular biology applications. This package provides an integrated system with versatile functions for high efficiency sequence analysis. You no longer need one program for restriction analyses and others for multiple sequence alignment, designing PCR primers, protein sequence analysis or drawing plasmids … DNAMAN carries out all these tasks for you.
DNAMAN
DNAMAN is a one-for-all software package for molecular biology applications. This package provides an integrated system with versatile functions for high efficiency sequence analysis. You no longer need one program for restriction analyses and others for multiple sequence alignment, designing PCR primers, protein sequence analysis or drawing plasmids … DNAMAN carries out all these tasks for you.
Modeller
MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (3,4), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.
Chimera
UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments. It is available free of charge for noncommercial use.
Chimera
UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments. It is available free of charge for noncommercial use.
MEGA
Molecular Evolutionary Genetics Analysis (MEGA) is computer software for conducting statistical analysis of molecular evolution and for constructing phylogenetic trees. It includes many sophisticated methods and tools for phylogenomics and phylomedicine. From the start, MEGA was intended to be easy-to-use and include solid statistical methods only
EMBOSS NEEDLE
EMBOSS Needle is used for pairwise alignment in bioinformatics. EMBOSS Needle reads two input sequences and writes their optimal global sequence alignment to file. Emboss Needle is available on the European Bioinformatics Institute < EMBL-EBI.
EMBOSS NEEDLE
EMBOSS Needle is used for pairwise alignment in bioinformatics. EMBOSS Needle reads two input sequences and writes their optimal global sequence alignment to file. Emboss Needle is available on the European Bioinformatics Institute < EMBL-EBI.
ENSEMBL
Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
HUMA
The Human Mutation Analysis (HUMA) database and web server. analysis of genetic variation in humans. HUMA integrates sequence, structure, variation, and disease data into a single, connected database. Users can upload their private variation datasets, which are automatically mapped to public data and can be analyzed. The interface provides data access and visualization, and RESTful Web API provides programmatic access to the data.
HUMA
The Human Mutation Analysis (HUMA) database and web server. analysis of genetic variation in humans. HUMA integrates sequence, structure, variation, and disease data into a single, connected database. Users can upload their private variation datasets, which are automatically mapped to public data and can be analyzed. The interface provides data access and visualization, and RESTful Web API provides programmatic access to the data.
looking for
Tools used in Programming
VISUAL STUDIO CODE
Visual Studio Code is an integrated development environment made by Microsoft for Windows, Linux and macOS. Features include support for debugging, syntax highlighting, intelligent code completion, snippets, code refactoring, and embedded Git. Users can change the theme, keyboard shortcuts, preferences, and install extensions that add additional functionality.
ATOM
Atom is a free and open-source text and source code editor for macOS, Linux, and Microsoft Windows with support for plug-ins written in JavaScript, and embedded Git Control. Developed by GitHub, Atom is a desktop application built using web technologies. Most of the extending packages have free software licenses and are community-built and maintained. Atom is based on Electron (formerly known as Atom Shell), a framework that enables cross-platform desktop applications using Chromium and Node.js. Atom is written in Coffee Script and Less, but much of it has been converted to JavaScript.
ATOM
Atom is a free and open-source text and source code editor for macOS, Linux, and Microsoft Windows with support for plug-ins written in JavaScript, and embedded Git Control. Developed by GitHub, Atom is a desktop application built using web technologies. Most of the extending packages have free software licenses and are community-built and maintained. Atom is based on Electron (formerly known as Atom Shell), a framework that enables cross-platform desktop applications using Chromium and Node.js. Atom is written in Coffee Script and Less, but much of it has been converted to JavaScript.
Rapid Miner
RapidMiner is a data science platform designed for enterprises that analyses the collective impact of organizations’ employees, expertise and data. RapidMiner’s data science platform is intended to support many analytics users across a broad AI lifecycle.
