Search Results for "amino" - Page 2
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Showing 84 open source projects for "amino"
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Software for visualization of point variability in pairwise sequence alignment FASTA format. Featuring GUI interface, this simple application enables insight into variation of nucleic and amino acids on specific loci. Current 1.1 version supports amino and nucleic acid alignments. There are 2 variations of this software. One is CLI based and the other one is GUI based. Read corresponding README files in order to get familiar with the software. Extract files and run the jar file!
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work in progress. ResidueFinder section is available for use, modified from MutationFinder. Residue finder, mutation, amino acid.
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Sequencia
Protein Primary Sequnece Analysis
The current work is focused on the Software Development of an Offline Tool for “PRIMARY-SEQUENCE ANALYSIS” with JAVA and open source resources. SEQUENCIA Tool is an offline Tool of Primary Sequence Analysis, which is quite prevalent Topic for Researchers all over the world. Sequence Name, Sequence Length, Absorbance, Net charge, Iso electric charge, Amino acid composition, Amino acid classification, Aliphatic Index, Instability Index, Average Hydropathy etc are the Primary Sequence Analysis... -
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nagnag
Identifyng and Quantifying NAGNAG Alternative Splicing
The NAGNAG alternative splicing is a regulatory process that controls the mRNA splicing from one gene. NAGNAG alternative splicing has attracted intensive attentions for last decades because of its unique property: inclusion or exclusion of three nucleotides results in difference of one or two amino acids in the final proteins. -
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The hub prediction model, HUBCENTRE, is the first one of its kind which enables the user to know whether a target protein is hub or non-hub based on the primary sequence information alone. The prediction of protein"hubs" was done using physiochemical, thermodynamic and conformational properties of amino acid residues from amino acid sequence. Our prediction results show that meaningful amino acid features can produce signature features for differentiating hubs from non-hubs. The classical...
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Protein Contact Matrix Generator
Command line application to generate contact matrix from proteins (3D)
A protein contact matrix is 2D representation of the distances between amino acid residues in a 3D protein structure. Protein Contact Map Generator (PCMGen) is a command line tool which takes protein 3D structures (PDB format files) as input and computes contact distances between two chains (from single or two different proteins). These matrix files can be further visualised as Contact Maps using other visualization tools/ programs (like R-heatmaps). Contact Maps can be used to understand... -
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GESPA
Accurately predicts disease association of single nucleotide mutations
GESPA (GEnomic Single nucleotide Polymorphism Analyzer) is a bioinformatics tool for classifying Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs). GESPA predicts if a nsSNP is pathogenic using reports from literature and various algorithms to assess conservation in orthologous and paralogous protein alignments. Using reports from literature, GESPA is also able to predict the phenotype of a nsSNP with high accuracy. The software can be used clinically to determine if observed nsSNPs are... -
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MNV Annotation Corrector
Multi-nucleotide Variation Annotation Corrector for NGS SNV callers
MAC is an Ad hoc software designated to fix incorrect amino acid predictions caused by multiple nucleotide variations (MNVs). These complex mutations consist of two or more consecutive nucleotide substitutions, but can only be detected in the format of several single nucleotide variations (SNV) by most variant callers and annotated separately, which likely leads to incorrect amino acid prediction when more than one mutated bases occur within the same protein codon. MAC screens through a list... -
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UniPyRange
Tool to fetch protein/DNA truncation constructs from Uniprot DB
Very simple python script which saves you the pains of counting the amino acids/DNA bases in fasta files from the Uniprot and NCBI RefSeq Database (1, 2). Lets say you want the amino acid sequence of range 128-387 from a 1000 amino acid protein - this script will help you to avoid counting mistakes by just showing you the specified sequence in amino acids and coding DNA base pairs (ideal for amplification primer design) of a specified Uniprot ID. - Requires BioPython (3) and Bioservices... -
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Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.
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NoiseRed
Protein alignment noise reduction
The project consists of reading alignments and removing noisy columns that fall under three requirements: 1) more than 50% are indels; 2) more than half of the proteins show unique amino acid in the given column; and, 3) if no amino acid appears more than twice in the column analyzed. The efficiency is tested by generating trees and comparing them with reference trees. Furthermore, a statistical analysis is performed to infer the suitability of the method. -
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StatAlign
An extendable statistical multiple alignment tool.
... on a single (probably suboptimal) alignment and bias towards the guide tree upon which the alignment relies. The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model. A broad range of models for nucleotide and amino acid data is included in the package and the plug-in management system ensures that new models can be easily added. -
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NOTE: developement of this project has moved to GitHub http://github.org/matthuska/biasviz/ BiasViz is a Java applet for visualization of amino acid bias in multiple sequence alignments.
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Protospacer
Rapid gRNA design and validation for CRISPR
... by gene ID, by exon/intron/UTR location, by sequence similarity, or by genomic co-ordinate. From here, users are able to evaluate potential off targeting, to export results in FASTA format or tabulated (e.g. for Microsoft Excel), and to connect to the Integrative Genomics Viewer (IGVref) and view target-sites in the context of genomic annotations, amino acid translations, and HT-Seq data (for off-target validation). We provide online video tutorials and a toy database from our main website. -
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SABLE is a public domain package for structural bioinformatics that can be used to predict from amino acid sequence secondary structure and solvent accessibility profiles in proteins (see Adamczak, Porollo and Meller, Proteins 56, 2004).
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AminoWin
Check if you win in amino
Aplikacja do sprawdzenia wygranej w konkursie Amino -
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provean
Predicting the functional effect of protein sequence variations
PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. The prediction is based on the change, caused by a variation, in the similarity of query sequence to closely related sequences collected through BLAST. -
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cmotif
A method for mining conditional phosphorylation motifs
Phosphorylation motifs represent position-specific amino acid patterns around the phosphorylation sites in the set of phosphopeptides. The discovery of phosphorylation motifs is a very valuable work in bioinformatics. Although several algorithms have been proposed to uncover phosphorylation motifs, the problem of efficiently discovering a set of significant motifs with sufficiently high coverage and non-redundancy still remains unsolved. In this paper, we propose an algorithm called C-Motif... -
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WISP
Weighted Implementation of Suboptimal Paths (WISP)
UPDATE: LATEST VERSION AT http://git.durrantlab.com//jdurrant/wisp Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site often many angstroms away. Traditionally, computational efforts have focused on the most optimal path... -
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Description: PseAAC-Builder is a cross-platform stand-alone program for generating protein pseudo-amino acid compositions. This is a bioinformatics program. It performs faster than the existing PseAAC server. Reference: [1] Pufeng Du, Shuwang Gu, Yasen Jiao. PseAAC-General: Fast Building Various Modes of General Form of Chou’s Pseudo-Amino Acid Composition for Large-Scale Protein Datasets. International Journal of Molecular Sciences 15 (2014) pp.3495-3506 [2] Pufeng Du, Xin Wang, Chao...
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SIFT (Sorting Intolerant From Tolerant) predicts whether an amino acid substitution affects protein function using sequence conservation and other features. SIFT is often applied to nonsynonymous variants and laboratory-induced missense mutations.
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Correct-O-Chem
Converts chemical formulae into their correct notation.
... (in any window) that enables you to enter either a codon or amino acid (name, 3 letter identifier or 1 letter identifier - NO SPACES) and displays the corresponding amino acid/codons. ctrl+` (the button to the left of the "1" - not apostrophe) or right-clicking on the tool tray icon and selecting Codon Calculator will activate the pop-up box. - Go to "https://code.google.com/p/correct-o-chem/" for a detailed "Read-Me" -
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PolyCTLDesigner
Python scripts for designing polyepitope T-cell immunogens
Given the peptides (T-cell epitopes) PolyCTLDesigner selects flanking sequences to optimize TAP-binding and joins resulting oligopeptides into a polyepitope in a way providing efficient liberation of potential epitopes by proteasomal and/or immunoproteasomal processing and minimizing the number of junctional epitopes. For constructing polyepitopes PolyCTLDesigner utilizes known amino acid patterns of proteasome cleavage and TAP-binding specificity. PolyCTLDesigner is also able to choose... -
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CDSbank
multi-sequence extraction, filtering & formatting
CDSbank is a database that stores both the protein-coding DNA sequence (CDS) and amino acid sequence for each protein annotated in Genbank. CDSbank also stores Genbank feature annotation, a flag to indicate incomplete 5’ and 3’ ends, full taxonomic data, and a heuristic to rank the scientific interest of a species. This rich information allows fully automated data set preparation with a level of sophistication that meets or exceeds manual processing. Defaults ensure ease of use for typical... -
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Sequence is a collection of nucleotides or amino acid residues which are connected with each other. Speaking biologically, a typical DNA/RNA sequence consist of nucleotides while a protein sequence consist of amino acids. In this project we aim to perform local sequence alignment between two nucleotide or amino acid sequences and find out structural or functional similarity. User can enter multiple DNA sequences. The given sequences are aligned by Sequence Alignment methodology - arranging...