Search Results for "protein" - Page 5
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Showing 363 open source projects for "protein"
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HubSpot is an AI-powered customer platform with all the software, integrations, and resources you need to connect your marketing, sales, and customer service. HubSpot's connected platform enables you to grow your business faster by focusing on what matters most: your customers.
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SKUDONET ADC, operates at the application layer, efficiently distributing network load and application load across multiple servers. This not only enhances the performance of your application but also ensures that your web servers can handle more traffic seamlessly.
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Protein Sequence Determination
Determines whether protein is mesophilic or thermophilic
The tool takes as input a protein sequence from the user, and determines whether it is mesophilic or thermophilic in nature. In addition, it also determines the percentage of acidic, basic, polar and non-polar residues in the sequence. -
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IPAS is a new and practial iterative progressive multiple sequence alignment algorithm, used to align protein sequences, which is a close variant of the MUSCEL algorithm. However, based on the gene sequences length, our algorithm starts either with the "kmer" distance table or with the "Dynamic Programming (DP)" distance table. The other steps of this algorithm include: generating a Guide-tree using UPGMA, multiple sequence alignments, "kimura" distance calculation from aligned sequences...
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BioFace is simple software for editing and analyzing DNA, RNA, and protein sequences that is written in Java using SWT and JFace as libraries. Opening GenBank, FASTA, EMBL, or simple sequence files and analizing these sequences can be done.
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JBioFramework
Growing suite of proteomics simulations for educational purposes
JBioFramework (JBF) is a set of two different chemical separations simulations (2D Electrophoresis and Mass Spectrometry) that are frequently used in chemistry, biochemistry and proteomics research. It is written in the Java programming language and will run on any and all systems that have the JVM installed. As we continue to develop the software over the coming months/years and attempt to quantify the success of our efforts with testing and reviews, user input is very important. Please... -
ChangeGear provides IT staff with the functions required to manage everything from ticketing to incident, change and asset management and more. ChangeGear includes a virtual agent, self-service portals and AI-based features to support analyst and end user productivity.
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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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AKtoolbox
Matlab Toolbox for coevolution analysis of multiple sequence alignment
AK Toolbox is a Matlab Toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) distributed under Simplified BSD License. The aim of AK toolbox is to provide a set of Matlab functions, which are independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis for MSA. At present, co-evolution methods available in this package are Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Covariance (ELSC), Mutual Information (MI), Observed Minus Expected... -
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Ever wanted to iterate through a range of Apex LE and HE setting to see what gives you the best answer? PLGS Threshold Inspector lets you do that.
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PSICOV
The unofficial binary for PSICOV: Protein Sparse Inverse COVariance
PSICOV (Protein Sparse Inverse Covariance estimation program) is a coevoultion algorithm applied to very large (typically >=1000 sequences) multiple sequence alignments for precise protein structural contact prediction. This is the unofficial precompiled Windows binary for PSICOV compiled by Chengxin Zhang at Fudan University. The source code is copyrighted by David T. Jones, University College London. -
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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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APBEST
APBEST--Analysis of Protein Block and Evaluation of Substitution Type
Program: APBEST--Analysis of Protein Block and Evaluation of Substitution Type Version:--v01:10B Author:(c)--Parth Sarthi Sen Gupta, Shyamashree Banerjee, Chittran Roy,Rifat Nawaz Ul Islam, Buddhadev Mondal, Arnab Nayek and Amal Kumar Bandyopadhyay*; Department of Biotechnology, The University of Burdwan, WB, India, 713104 -
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In the program the user will be able to do one of the three functions, which are changing DNA to RNA, changing DNA to a protein, and do a DNA duplication. Introduction.
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PrAS
predict protein amidation sites
This predictor is developed to predict amidation sites based on support vector machine (SVM) classifier. It is supplied in source code form along with the required data files and run under the linux. The input is a protein sequence file (fasta format) by Tong Wang and Wei Zheng (tongwang.scu@gmail.com and jlspzw139@sina.com) Notice:You should download all zip file in this project! -
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hadiproject
The following program measures the percentage similarity of protein se
This program is a multiple sequence comparison program for proteins. Scientists have pursued comparing sequences of proteins because it allowed them to have structural evidence of the species’ physical features without even having to look at the species, just by using the genetic sequence of their proteins. Comparing sequences also helps hypothesize the future for any evolutionary changes a certain species can go through based on its protein sequence compared to animals of the same species. -
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GenomeDatabase
For creating a local database of reference genomes
Genome Database - A tool to create a local database of reference genome sequences Usage: java path/to/GenomeDatabase.jar [options] By Marc Strous, 2016 This tool enables you to download fasta files of protein and RNA sequences encoded in reference genomes at NCBI. You can select relevant genomes with a set of queries. Each query has four fields, separated by comma's. Example of a queries are: superkingdom,Bacteria,genus,ftp superkingdom,Archaea,genus,ftp superkingdom,Eukaryota,phylum,ftp... -
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RAPSearch2
Reduced Alphabet based Protein similarity Search
RAPSearch2 is a tool for fast protein similarity searches. RAPSearch2 searches short DNA sequences (reads) or protein sequences against protein database, achieving >100 times speedup as compared to BLASTX (for reads of ~100bp), or >1000 times speedup over BLASTX in the accelerating mode (option "-a"). RAPSearch2 utilizes reduced amino acid alphabet and flexible seed so that seeds of various lengths with mismatches can be identified quickly by hashing. -
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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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PDBManip
PDBManip is a free program for editing PDB (Protein Data Bank) Files
PDBManip is a free program for editing and manipulating PDB (Protein Data Bank) files. It has a graphical user interface and it is provided as an executable file for running on Windows® operating systems. There is a bunch of free programs on the internet for the same purpose. What discriminate between PDBManip and those programs is that PDBManip uses AngelScript language which is very similar to C/C++ language, to write scripts to do our editing tasks. I know that the text-manipulation script... -
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EBprotV2
Bayesian Analysis of labeling-based Quantitative Proteomics Data
EBprotV2 is an extension to the existing EBprot (version 1) which adopts a more flexible non-parametric mixture model. It serves as an differential expression analysis tool which takes into account the direct peptide to protein hierarchy which differs from the usual analysis which occurs at the protein-summary level. The tool is implemented in C++ which minimize computational time and also, incorporates an additional module which help users to generate comparison ratios between groups... -
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PANTHER project: software for modeling of protein sequence and function evolution, and tools for applying these data to the analysis of genome data, expression data and coding SNPs. Details available at http://www.pantherdb.org.
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Genix: Bacterial Genome Annotation Pipel
A automated annotation pipeline for bacteria / archea genomes
Genix is an online automated pipeline for bacterial genome annotation that integrates the programs Prodigal, BLAST, RNAmmer, tRNAscan-SE, INFERNAL, ARAGORN and HMMER, and the databases Uniprot, Antifam and Rfam. -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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geneslider
Gene Slider for Alignment Visualisation
Gene Slider can be used to visualize conservation and entropy of aligned DNA and protein sequences by presenting them as one long sequence logo. The presented sequence logo can be zoomed in and out. It can also display motifs in alignments. A built-in search function can be used to find motifs. Gene Slider is available online on the Bio-Analytic Resource and for download here. -
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KA-predictor
lysine acetylation site prediction
This predictor is developed to predict species-specific lysine acetylation sites based on support vector machine (SVM) classifier. It is supplied in source code form along with th e required data files and run under the linux. The input is a protein sequence file (fasta format).