Search Results for "proteins" - Page 3
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Showing 170 open source projects for "proteins"
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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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protcalc
Protein Calculator
Determines parameters for proteins based on their sequence, including estimates of pI's. -
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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IMPORTANT NOTE: This project has been migrated to GitHub and is no longer maintained here.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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Multiple Sequence Alignment using DP
Dynamic Programming (DP) is widely used in Multiple Sequence Alignment
... sequences. MSA is also often used for constructing evolutionary trees from DNA sequences and for analyzing the structures to help in designing new proteins. Usually, to solve an MSA problem is to find an alignment of multiple sequences with the highest score based on a given scoring criterion among sequences. -
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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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This project includes perl scripts to perform transcriptome reconstruction in bacteria (operons and UTRs). The software was applied to the transcriptome reconstruction of the species Methanococcoides burtonii, if you use it please refer to the following paper (Taha et al., Single TRAM domain RNA-binding proteins in Archaea: functional insights from Ctr3 from the Antarctic methanogen Methanococcoides burtonii - Submitted). The approach used is based on previous results: - Campanaro S, et al...
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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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PrinCCes: continuity-based geometric decomposition and systematic visualization of the void repertoire of proteins
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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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Stochastic Rule Builder (SRB)
Modeling framework for capturing positional and temporal dynamics
We present a modeling framework aimed at capturing both the positional and temporal behavior of transcriptional regulatory proteins. There is growing evidence that transcriptional regulation is the complex behavior that emerges not solely from the individual components, but rather from their collective behavior, including competition and cooperation. Our framework describes individual regulatory components using generic action oriented descriptions of their biochemical interactions with a DNA... -
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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... -
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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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... classification method, Support Vector Machines (SVM), is used to develop a tool to discriminate between hub and non hub proteins. Funding from Department of Information Technology,Govt. of India, (DIT/R&D/B10/15(23)2008, dated 07/09/2010), is acknowledged.
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DiSir
In-silico digestion of proteins.
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jChIP
Graphical environment for exploratory ChIPSeq data analysis
jChIP is a GUI-based Java application for ChIP-Seq data analysis. It was created to build binding profiles between proteins and loci in the genome. In addition it computes statistics of the number of loci/positions containing specified amount of tags. jChIP is able to load data in several common formats (SAM, BAM, WIG, BED, Bowtie) and download loci definitions directly from the Ensembl database. http://www.biomedcentral.com/1756-0500/7/676