Search Results for "proteins" - Page 2
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Showing 114 open source projects for "proteins"
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GlycoPAT
Comprehensive, open-source tool for glycoproteomics MS data analysis
GlycoPAT is a modular, open-source MATLAB based toolbox for shotgun mass spectrometry based glycoproteomics data analysis. This program provides a novel platform for the streamlined analysis of traditional LC-MSn based high-throughput experimental data for the identification of site-specific N- and O-linked glycosylation on various proteins. More details are available at https://www.VirtualGlycome.org/glycopat Source code also available at https://github.com/kaichengub/GlycoPAT If you... -
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datasw
datasw, a tool for rapid processing of HPLC-SAXS data.
... experiment using a sliding window of a user-specified size, calculates overall parameters (I(0), Rg, Dmax and MW) and predicts the folding state (folded/unfolded) of the sample. Applications of DATASW are illustrated for several proteins with various oligomerization behaviors recorded at different beamlines. If you use DATASW in your work, please, cite: Shkumatov A.V. & Strelkov S.V. (2015) Acta Cryst. D71, 1347–1350 -
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MSqBAT
Label-free protein quantification for LC-MS
MSqBAT is a freely-available all-platform software application for label-free quantification of proteins from LS-MS data. It was developed in the lab of Dr. Christoph Rösli at the Heidelberg Institude for Stem Cells and Experimental Medicine (HI-STEM) and the German Cancer Research Center (DKFZ). It’s main features are 1) Label-free, MS1-based quantification 2) Support both LC-MALDI-MS- as well as LC-ESI-MS data 3) Supports both GeLC-MALDI-MS- and GeLC-ESI-MS data 4) Convenient, graphical... -
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local alignment 374
software for insertion in the local alignment for new combinations
This software is used to insert in the combinations of the proteins as it make with different types of bases as A ,T ,C etc and we take two combinations as the in put and find the alignment between them and then we enter a new element in the combination and find another combination with respect to it as there are lot of methods of having insertion use of one of these methods make this software . It is only university project so may be it is possible you to find an error in so just email it . -
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HGPEC
A tool for gene and phenotype prioritization and evidence collection
.... This plugin can prioritize candidate genes and phenotypes by employing a heterogeneous net-work consisting a network of genes/proteins and a phenotype similarity network. Based on the rankings, novel putative gene-disease and disease-disease associations can be identified. These associations can be supported with network-based visualization and evidences and annotations from biomedical data -
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KAPPA (Key Aminoacid Pattern-based Protein Analyzer) is a sequence search program dedicated to the discovery and clustering of proteins defined by a key aminoacid pattern.
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Community profiling (CP) is a guilt-by-association approach for predicting functional associations between proteins: two proteins are predicted to be associated if they share similar presence and absence profiles (called community profiles) across microbial communities. Community profiling is conceptually similar to the phylogenetic profiling approach to functional prediction, however with fundamental differences. This package provides different profile construction methods and correlation...
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PPA D
A method for predicting the locations of protein antigenic determinant
A computerized method for predicting the locations of protein antigenic determinants is presented, which requires only the amino acid sequence of a protein, and no other information. This procedure has been used to predict the major antigenic determinant of the hepatitis B surface antigen, as well as antigenic sites on a series of test proteins of known antigenic structure. The method is suitable for use in smaller personal computer, and is written in C++ in order to make it available... -
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mRNA
mRNA sequencing and translating to proteins
The use is prompt to input a DNA sequence which gets transcribed into mRNA and translated into proteins. The user can also input the RNA sequence which will give the DNA associated with it and will also translate it to proteins. The program utilizes the fun and easy to use GUI to make RNA sequencing accessible to all. -
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PeaksAndValleys
Peaks and Valley detection using NGS data
Active regulatory elements in eukaryotic genomes are typically associated with nucleosome-depleted regions that are hypersensitive to digestion by nonspecific endonucleases. Techniques which distinguish active regulatory elements by virtue of this include micrococcal nuclease digestion of chromatin (MNAse-seq), which preferentially depletes DNA which is not tightly bound by proteins, and formaldehyde-assisted isolation of regulatory elements (FAIRE-seq), which enriches for sequences which... -
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EBprot
Bayesian Analysis of labeling-based Quantitative Proteomics Data
EBprot implements a hierarchical mixture model directly representing the peptide-protein map. The model fit is used to score differential expression of proteins in a (signed) probability scale based on reproducible quantification over multiple peptides. The package takes as input a data matrix with each row containing the data for one peptide, including protein and peptide identifier and peptide ratio(s), and returns the protein-level score table with PPscore, BFDR, Posterior Odds score... -
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gDNA-Prot
DNA-binding protein prediction software
This program will predict the DNA-binding proteins when input a protein sequence (Fasta format), it is supplied in source code form along with the required data files and run under the windows. -
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PingPongPro
Find ping-pong signatures like a pro
IMPORTANT NOTE: This project has been migrated to GitHub and is no longer maintained here. Please refer to: https://github.com/suhrig/pingpongpro Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs, predominantly active in the germ line. There, they limit the detrimental effect of transposons on the genome. They do so by forming a complex with Piwi proteins. The complex binds and then cleaves mRNA molecules of active transposons. The resulting mRNA fragments induce... -
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PanCGP
PanCGP: Pangenome and Comparative Genome Analysis Pipeline tool
Pan-genome and Comparative Genome analysis Pipeline tool is a high performance parallel computing analysis tool. The aim of developing this high performance and scalable pipeline is to reduce the time cost of calculating the pan-genomes from the given dataset of protein sequences of bacterial strains. The pipeline is able to compute pan-genome analysis from unpublished data-sets as well. Those results are interpreted in the form of pan-genome, core genome/proteins, dispensable genes/proteins... -
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NGS-TOOLBOX
Handy tools to process/analyze next generation sequencing (NGS) data
... purposes you can cite the following methods paper: Rosenkranz D, Han CT, Roovers EF, Zischler H, Ketting RF. Piwi proteins and piRNAs in mammalian oocytes and early embryos: From sample to sequence. Genomics Data 2015 5:309-313. -
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LowMACA
Low frequency Mutation Analysis via Consensus Alignment
... medicine. To overcome this difficulty, we have implemented LowMACA (Low frequency Mutation Analysis via Consensus Alignment), a new method able to assess specific characteristics of rarely mutated genes that show patterns of positive selection. LowMACA aggregates and analyzes the mutational patterns of several genes whose encoded proteins have a high level of sequence similarity or share specific protein domains. -
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... are.... (1) Configured for 4 open source algorithms to perform database searching for peptide identification. Any combination of the 4 algorithm can be chosen. (2) Lists out the genome search specific peptides(Novel peptides). (3) Spectral matches can be visualized for the quality assessment. (4) Lists out the novel proteins and changes in the existing protein annotations. (5) A Visual genomic context of the novel peptides can also be generated.
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Fitness Trainer
Your own personal virtual trainer for Body & Mind.
/*Requirement: Java Installed*/ With this project the user can measure if he/she has a healthy weight then then go on exploring the application. This project is perfect for every individual who want to become fit physically and mentally. Common questions like How to lose weight, gain weight increase height, build body, lose fat, run fast, Mindfulness, different types of exercises, What to eat and what not to, everything is available. The user needs to keep in mind that content of this... -
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The Protein Similarity Network
Human protein similarity network used to predict drug safety.
This is the protein similarity network - PSIN. Here, the nodes are human proteins and they are linked only if they share considerable sequence similarity. We found that this network is particularly useful to distinguish approved from problematic drug-targets. Here you also find the complete set of programs and datasets we used for this purpose. Free to help further test and develop this project. Your help and expertise are much appreciated ! If you have any questions, please do... -
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eSBMTools
python tools for enhanced native structure-based modeling
eSBMTools: python tools that assist the setup and evaluation of native structure-based simulations of proteins and nucleic acids, both at the Cα and all-atom level. The tools interface with GROMACS and support its standard output formats. Information from other sources like bioinformatics or experimental data can be added to the standard native structure-based model (SBM). Publication to be cited: Benjamin Lutz, Claude Sinner, Geertje Heuermann, Abhinav Verma, and Alexander Schug. eSBMTools... -
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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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merlin is an user-friendly Java application that performs the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs several steps of the reconstruction process, including the functional genomic annotations of the whole genome. Moreover, merlin includes tools for the identification and annotation of transport proteins encoding genes, as well as the generation of transport reactions for such carriers. Also, merlin includes tools...
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StrainControl
StrainControl - wet-lab PC inventory system
StrainControl is maximized with features that will help you manage everything in the lab: -Manage strains, cell-lines, proteins, plasmids, oligos, chemicals, inventories etc. -Share your database on a network -Rename modules, column and text fields -Hide columns that are not used -Create user accounts (read/write/admin etc) -Import or export using user-friendly guides -Auto-update and free support 24/7 -
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newDNA-Prot
dna binding protein predict soft
newDNA-Prot by Wei Zheng (jlspzw139@sina.com) This program will predict the DNA-binding proteins when input a protein sequence (Fasta format), it is supplied in source code form along with the required data files and run under the windows. we firstly need to download the newDNA-Prot.tar. After decompressing this files,we must firstly download the fortran-windows (https://gcc.gnu.org/wiki/GFortranBinaries/) and install the gfortran-windows-20140523.exe.(In this program, the comprehensive...