Search Results for "proteins" - Page 4
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Showing 175 open source projects for "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 -
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pipasic
pipasic: Protein Abundance Correction in Metaproteomic Data
Metaproteomic analysis allows studying the interplay of organisms or functional groups and has become increasingly popular also for diagnostic purposes. However, difficulties arise due to the high sequence similarity between related organisms. Further, the state of conservation of proteins between species can be correlated with their expression level which can lead to significant bias in results and interpretation. These challenges are similar but not identical to the challenges arising... -
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DESN
Differential activE sub-Network (DEN): R/Bioconductor based package
Living cells are complex, dynamic, self-regulatory, interactive systems, showing differential states across time and space. Complexity of cellular systems is highlighted with the multi-layered regulatory mechanisms involving the interactions between bio-molecules (such as DNA, RNA, mi-RNA and proteins). These interactions are analyzed in the form of static networks. Likewise, number of experimental techniques like microarray, RNASeq allows quantification of cellular dynamics and aid... -
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NemCX
Searches for NCX motifs from nematode proteins
Web-based tool that uses protein alignments from divergent nematode species to identify candidate NCX-type proteins from nematodes Returns: 1) input residue composition; 2) position of candidate match; 3) the match; 4) identity (%); 5) links to genes in C. elegans that encode proteins with the same match Link to NemCX: http://ohalloranlab.net/NemCX.html -
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diggit
R package for DIGGIT algorithm
DIGGIT identify genetic variants associated with drivers of specific physiopathologic states. I computes the statistical association between the presence of genetic variants (CNV or SNP) and the activity of proteins driving physiologic or pathologic phenotype. It requires large gene expression and genetic variants datasets and depends on context-specific regulatory networks including transcriptional interactomes (usually reverse engineered by the ARACNe algorithm) and post-translational... -
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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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CViT - Chromosome Viewing Tool. A collection of Perl scripts that enable quick visualizations of features on linkage groups, psuedochromosomes or cytogenetic maps. Intended for whole-genome views of data but can be used to create images of single chromosomes/linkage groups, contigs, or BACs, or even proteins -- any feature that has a location on a backbone. Handles most standard genetic/genomic coordinate systems. Reads GFF3 data and produces a PNG or SVG image.
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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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Just_Annotate_My_Genome
Comprehensively annotate your non-model species genome.
Uses an existing exonerate output or just predicted proteins (e.g. from Transdecoder or just a FASTA file) to prepare gene prediction inputs for Augustus, SNAP and geneid. Exonerate is run (enabled via AAT) if it is not provided. GTF file is produced to judge quality of annotation. Sorts out high quality alignments from those that don't meet the criteria. -
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DNATweezer
A suite of BioPerl wrappers for manipulating DNA and protein sequences
DNATweezer is a suite of Perl scripts for manipulating DNA and proteins sequences. These scripts provide command-line access to the most frequently used BioPerl DNA object methods e.g. reverse-complement and translation of DNA sequences, slicing a sequence alignment, rerooting a phylogenetic tree, and calculating diversity of a population of DNA sequences. -
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PyInteraph
analysis of interaction networks in structural ensembles of proteins
... be thoroughly analyzed using included network analysis tools, which are able to point out the most important features of the network for the discovery of paths of structural communication in proteins. The tool works best together with the xPyder PyMOL plugin ( http://xpyder.sourceforge.net ), which allows for further analysis and easily understandable representation of the calculated networks and graphs. -
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QUDeX-MS
Hydrogen/deuterium exchange estimation for isotopic fine structure MS
Hydrogen-deuterium exchange coupled to mass spectrometry permits analysis of structural dynamics, stability, and molecular interactions of proteins. Resolving isotopic fine structure during mass spectrometry has been recently demonstrated to allow direct detection and quantification of deuterium incorporation distinct from peaks corresponding to non-deuterium incorporated natural abundance heavy isotopomers. Here, we present a graphical tool that allows for a rapid and automated estimation... -
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xPyder PyMOL Plugin
Analyze and visualize coupled residues and their networks in proteins
xPyder is a PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images. xPyder identifies networks (using concepts from graph theory, such as hubs and shortest path searching), compares matrices and focuses the analysis on relevant information by filtering the data... -
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FIAP
Fully Integrated Annotation Pipeline
FIAP (Fully Integrated Annotation Pipeline) is a fast bacterial genome multithreading annotation pipeline written in Perl that detects genes coding for proteins, tRNAs, and rRNAs (5S, 16S and 23S). FIAP also allows users to include an infinite number of custom databases. This feature is extremely valuable because it allows users to add a personal “flavor” to the annotation and optimize the process for a specific bacterial genome. FIAP can annotate single and multiple sequences, which allows... -
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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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VarImpact
Extracting effects of mutations on molecular properties from text.
Genetic variants alter cellular behavior in a variety of ways, changing biochemical properties of DNA, mRNA, and proteins. Many large-scale sequencing projects are under way to detect human variation in health and disease. Although broad disease associations can be discovered by GWAS studies, the low-level impact of mutations is hardly available in structured form. The results of thousands of small-scale experiments, on the other hand, are present in the literature and discuss observations made... -
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AS-peak
ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq
Unlike DNA, RNA abundances can vary over several orders of magnitude. Thus identification of RNA-protein binding sites from high throughput sequencing data presents unique challenges. While peak identification in CHIP-Seq data has been extensively explored, there are few bioinformatics tools tailored to peak calling on the analogous datasets for RNA-binding proteins. Here we describe ASPeak, an implementation of an algorithm that we previously applied to detect peaks in Exon Junction Complex... -
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This is the tool for the project of "Classifying substrates transported bye membrane transporters proteins using neighboring genes".
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.... Observing that the size of true orthologs across species is small comparing to the total number of proteins in all species, we take a dierent approach based on a precompiled list of homologs identified by KO terms. Applying this approach to S. cerevisiae (yeast) and D. melanogaster (+y), E. coli K! and S. typhimurium, E. coli K! and C. crescenttus, we analyze all clusters identi)ed in the alignment. (e results are evaluated through up-to-date known gene annotations, gene ontology (GO), and KEGG ...
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CodaChrome
CodaChrome: The Pan-Genomic Explorer
CodaChrome is a tool for visually exploring how the proteome of a bacterium of interest relates to every other finished bacterial genome in GenBank. -
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apmsWAPP
Pre- and Postprocessing For Affinity Purification Mass Spectrometry
The reliable detection of protein-protein-interactions by affinity purification mass spectrometry (AP-MS) is a crucial stepping stone for the understanding of biological processes. The main challenge in a typical AP-MS experiment is to separate true interaction proteins from contaminants by contrasting counts of proteins binding to specific baits with counts of negative controls. -
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apmsWAPP
Pre- and Postprocessing For Affinity Purification Mass Spectrometry
The reliable detection of protein-protein-interactions by affinity purification mass spectrometry (AP-MS) is a crucial stepping stone for the understanding of biological processes. The main challenge in a typical AP-MS experiment is to separate true interaction proteins from contaminants by contrasting counts of proteins binding to specific baits with counts of negative controls. -
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RASPnmr
Protein NMR backbone resonance assignment
RASP uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy. This enables rapid determination of highly accurate assignments on the basis of minimal experimental datasets, even for spectroscopically challenging proteins. RASP takes as input spin systems assembled on the basis of an arbitrary set of conventional triple-resonance NMR experiments. Uniquely, RASP is capable of extensive assignments even in the abscence... -
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adhesin prediction tools
Standalone version of adhesin prediction tools
This project provides users with standalone version of adhesin prediction tools- SPAAN: a software program for prediction of adhesins and adhesin-like proteins, MAAP: Malarial adhesin and adhesin-like proteins predictor and FungalRV adhesin predictor. The individual readme with each software contains the detailed instructions of software installation and usage procedures. These softwares are artificial intelligence based non-homology methods developed to aid identification of novel adhesins... -
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Arpeggio
Harmonic analysis of ChIP-seq experiments
Researchers generating new genome-wide data in an exploratory sequencing study can gain biological insights by comparing their data with well-annotated datasets possessing similar genomic patterns. Data compression techniques are needed for efficient comparisons of a new genomic experiment to large repositories of publicly available profiles. Arpeggio allows us to efficiently compare numerous ChIP-seq datasets consisting of many types of DNA-binding proteins collected from a variety...