Multiple sequence alignment software tools | Protein data analysis
Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
A versatile multiple sequence alignment (MSA) method suitable for aligning virtually any type of biological sequences. T-Coffee provides more than a simple sequence aligner; rather it is a framework in which alternative alignment methods and/or extra information (i.e., structural, evolutionary, or experimental information) can be combined to reach more accurate and more meaningful MSAs.
A package for making multiple sequence alignments of amino acid or nucleotide sequences, quickly and accurately. Clustal Omega can deal with very large numbers (many tens of thousands) of DNA/RNA or protein sequences due to its use of the mBED algorithm for calculating guide trees. This algorithm allows very large alignment problems to be tackled very quickly, even on personal computers.
Offers a platform for multiple sequence alignment. PRALINE includes various alignment optimization strategies to address the different situations that call for protein multiple sequence alignment: global profile preprocessing, homology-extended alignment, secondary structure-guided alignment, and transmembrane aware alignment. The software allows the sequences in the alignment to be represented in a dendrogram to show their mutual relationships according to the alignment.
Assists users in aligning transmembrane proteins. TM-Aligner is a protein sequence alignment tool that provides instant result for alignment. It can perform multiple sequence alignment of unlimited number of transmembrane proteins of any length. It permits to visualize MSA in different color schemes and with variety of options. It also provides an option to select and delete sequences from final alignment.
Finds the multiple sequence alignment (MSA) with the maximum expected accuracy (MEA). PicXAA is a probabilistic non-progressive alignment algorithm which takes a greedy approach to probabilistically build up the MSA, by starting from confidently alignable regions (with high similarities) and proceeding toward less confident regions (with lower similarities). By building up the MSA from the confidently alignable regions, the software reduces the risk of propagating the alignment errors made at the early stage to the final alignment.
Allows multiple alignment of DNA, RNA and protein sequences. DIALIGN-TX, an extension of the multiple-alignment program DIALIGN, adapts the progressive approach to multiple alignment to the fragment-based alignment as used in DIALIGN. The web interface allow users to select various parameter values. The downloadable program version contains more options and adjustable parameters.
Provides access to a variety of public and in-house bioinformatics tools. The MPI Bioinformatics Toolkit integrates a selected set of most useful methods for the analysis of protein sequences and structures. It offers more of 50 interconnected tools, so that the results of one tool can be forwarded to other tools. It also includes a useful platform for teaching bioinformatic enquiry to students in the life sciences.
Provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). It is described in terms of a solution that brings together a number of protein analysis tools at a single web server. SMS is a very powerful tool which enables a quick estimate of the level of engagement for each amino acid within its own protein chain and functionally more importantly, in the mechanism of binding to substrate and/or inhibitor.
Allows evaluation of Multiple Sequence Alignment (MSA) using structural information. iRMSD-APDB, provided a data set containing at least two structures, returns an evaluation of the considered alignment that takes into account the quality of the implied structural superposition. The software is suitable for evaluating and comparing sequence alignment methods without a need for pre-established reference alignment collections. It is part of the T-Coffee web-server.
Allows multiple sequence alignment. Probalign computes maximum expected accuracy multiple sequence alignments (MSA) using partition function posterior probability. The web server, eProbalign, automatically computes Probalign alignment and allows visualization of the alignment, generation of images, and manipulation of the output by average column posterior probabilities. The standalone software can be used for large datasets (more than 100 sequences).
Aligns a set of protein–protein complexes in 3D space. MAPPIS is a web application that recognizes the shared spatially conserved interaction patterns. It detects spatially conserved patterns of interactions even when there is no sequence or fold similarity between the corresponding proteins. This method considers the physico-chemical properties formed by groups of atoms and are independent of the overall similarity in the protein sequences or folds.
Allows users to perform the alignment of multiple related sequences. MultAlin is a platform based on an algorithm exploiting progressive pairwise alignment that considers relationships that can exist among some subsets of sequences. The application includes options to set the desired output format and its size and colors as well as configure personalized alignment parameters such as the number of iterations and the gap penalties required.
Provides a protein progressive multiple alignment tool. ProbCons is a pair-hidden Markov model-based progressive alignment algorithm. This method works by (1) computing posterior probability matrices, (2) computing expected accuracies for each pairwise comparison, (3) applying the probabilistic consistency transformation, (4) computing an expected accuracy guide tree, and (5) performing progressive alignment.
A state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. MSAProbs can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input datasets. MSAProbs-MPI is a distributed-memory parallel version of the multithreaded MSAProbs tool that is able to reduce runtimes by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on a cluster with 32 nodes (each containing two Intel Haswell processors) shows reductions in execution time of over one order of magnitude for typical input datasets. Furthermore, MSAProbs-MPI using eight nodes is faster than the GPU-accelerated QuickProbs running on a Tesla K20.
Allows user to analyze any closely related sequences. eShadow studies multiple protein alignments and identifies functional elements. It incorporates two distinct approaches for finding functional elements: Hidden Markov Model Islands (HMMI) and Divergence Threshold (DT) scans of multiple (or pairwise) sequence alignments. This tool is useful to highlight regions with coding potential.
Addresses the problem of alignment of very large datasets, potentially containing fragmentary data. UPP can align datasets with up to 1,000,000 sequences. UPP produces highly accurate alignments for both nucleotide and amino acid sequences, even on ultra-large datasets or datasets containing fragmentary sequences.
Provides a useful method for automated multiple alignment of multi-domain proteins. ProDA is an integrated alignment methodology designed to (i) computes local alignments for every pair of sequences, (ii) clusters such alignments into blocks of approximately globally alignable subsequences, (iii) determines block boundaries, (iv) resolves inconsistencies between pairwise alignments and finally (v) multiply aligns these blocks.
Performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. The PSI/TM-Coffee web server is part of the T-Coffee web platform; its access is free and unrestricted, without login procedure.