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PRALINE / Profile ALIgNmEnt
A toolkit for multiple sequence alignment. PRALINE provides 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.
TM-Aligner / Transmembrane Membrane proteins-Aligner
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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.
PicXAA / ProbabilistIC maXimum Accuracy 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.
SMS / STING Millennium Suite
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.
MAPPIS / Multiple Alignment of Protein-Protein InterfaceS
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.
MSAProbs-MPI
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.
PVS / Protein Variability Server
Provides absolute sequence variability estimates ‘per site’ in a multiple protein-sequence alignment (MSA). PVS returns the selected reference sequence with the variable positions masked, as well as the sequence fragments containing only non-variable residues. It aims to facilitate structure-function studies and de novo epitope discovery. This tool returns results that facilitate the design of vaccines driven by epitope discovery against pathogenic organisms.
SigniSite
An online application for subgroup-free residue-level genotype-phenotype correlation. In contrast to similar methods, SigniSite does not require any pre-definition of subgroups or binary classification. Input is a set of protein sequences where each sequence has an associated real number, quantifying a given phenotype. SigniSite will then identify which amino acid residues are significantly associated with the data set phenotype. As output, SigniSite displays a sequence logo, depicting the strength of the phenotype association of each residue and a heat-map identifying 'hot' or 'cold' regions.
PSI/TM-Coffee
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.
PTMap
Recognizes full-spectrum post-translational modifications (PTMs) and polymorphisms. PTMap supplies an algorithm able to determine protein polymorphisms as well as to map sites of unspecified PTMs. The application includes three main characteristics: (i) mass spectrometry (MS) peak selection, (ii) automatic mass-shift calibration, and (iii) exclusive site localization. In addition, the algorithm can facilitate the elimination of false positives by stressing unmatched peaks added to manual verification rules.
SATCHMO / Simultaneous Alignment and Tree Construction using Hidden Markov mOdels
Constructs simultaneously a tree and a set of multiple sequence alignments, one for each internal node of the tree. SATCHMO generates profile hidden Markov models (HMM) at each node; these are used to determine branching order, to align sequences and to predict structurally alignable regions. SATCHMO is shown to perform comparably to ClustalW and the UCSC SAM HMM software. Results using SATCHMO to identify protein domains are demonstrated on potassium channels, with implications for the mechanism by which tumor necrosis factor alpha affects potassium current.
MAPGAPS / Multiply-Aligned Profiles for Global Alignment of Protein Sequences
Uses a multiple-profile alignment to ‘map the gaps’ (i.e. the insertions and deletions, both large and small) between distantly related proteins. The multiple-profile alignment serves both as a query for detecting and classifying related sequences and as a template for globally aligning the sequences to each other. Creating and maintaining multiple-profile alignments and searching with them in this way has several advantages. In particular, this facilitates rapid detection and accurate alignment of up to a million or more related protein sequences, yet is equally useful and accurate for alignment of small sequence sets.
MP-T / Membrane Protein Threader
Performs sequence to structure alignment for the homology modelling of membrane proteins. The Membrane Protein Threader is a progressive multiple alignment method specifically use on membrane protein sequences. The accuracy of this method is derived from its effective use of information about accessible surface area, membrane positioning and secondary structure. Incorporation of environment awareness into this aligner may yield even larger improvements in the quality of membrane protein models.
SIBIS
The prediction of protein coding genes is a major challenge that depends on the quality of genome sequencing, the accuracy of the model used to elucidate the exonic structure of the genes, and the complexity of the gene splicing process leading to different protein variants. As a consequence, today's protein databases contain a huge amount of inconsistency, due to both natural variants and sequence prediction errors. SIBIS is designed to detect such inconsistencies based on the evolutionary information in multiple sequence alignments. A Bayesian framework, combined with Dirichlet mixture models, is used to estimate the probability of observing specific amino acids and to detect inconsistent or erroneous sequence segments.
KMAD / Knowledge based Multiple sequence Alignment for intrinsically Disordered proteins
Aligns and annotates intrinsically disordered proteins (IDPs). KMAD augments the substitution matrix with knowledge about posttranslational modifications, functional domains, and short linear motifs. MSAs produced with KMAD describe well conserved features among IDPs, tend to agree well with biological intuition, and are a good basis for designing new experiments to shed light on this large, understudied class of proteins.
PASTASpark / Practical Alignments using SATé and TrAnsitivity
Allows to improve the performance of the alignment phase of practical alignments using saté and transitivity (PASTA). PASTASpark allows to execute PASTA on a distributed memory cluster making use of Apache Spark (a big data engine). Apache Spark permits to improve the performance of the alignment phase of PASTA. It guarantees scalability and fault tolerance, and contributes to obtain multiple sequence alignments (MSAs) from very large datasets in reasonable time.
MIToS.jl / Mutual Information Tools for protein Sequence analysis in the Julia language
An environment for mutual information analysis. MIToS is also a framework for protein multiple sequence alignments (MSAs) and protein structures management in Julia language. It integrates sequence and structural information through SIFTS, making Pfam MSAs analysis straightforward. MIToS streamlines the implementation of any measure calculated from residue contingency tables and its optimization and testing in terms of protein contact prediction.
BaCoCa / BAse COmposition CAlculator
Identifies biases in aligned sequence data which potentially mislead phylogenetic reconstructions. BaCoCa allows a parallel determination of a suite of different statistical properties of alignments for complete concatenated amino acid and nucleotide data sets as well as for user-defined gene partitions and taxon subsets in one single process run prior to any tree reconstruction. Its results can be easily used for further analyses in programs like Excel or statistical packages like R.
GlycoSiteAlign
Aligns amino acid sequences of variable length surrounding glycosylation sites depending on the knowledge of glycan structure. GlycoSiteAlign is an exploratory resource intended for the identification of characteristic amino acid patterns of unique glycan-protein interactions. It uses data from the UniCarbKB and UniProtKB databases and it is hosted on ExPASy, the Swiss Institute of Bioinformatics resource portal. The tool can recognize amino acid patterns and/or residues usually “diluted” or masked in alignments that take into consideration only the glycosylation type.
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