Search Results for "protein protein interaction" - Page 2

Showing 66 open source projects for "protein protein interaction"

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  • 1
    MGEScan is a suite of two software tools MGEScan-LTR and MGEScan-non-LTR. MGEScan-LTR is a software that can identify new LTR retrotransposons without relying on a library of known elements. It uses approximate string matching technique and protein domain analysis to detect intact LTR retrotransposons. In addition, it identifies partially deleted or solo LTRs using profile Hidden Markov Models (pHMMs). MGEScan-non-LTR is a software for the identification of non-LTR retrotransposons...
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  • 2
    FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
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  • 3
    PseAAC-Builder
    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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  • 4
    ADDA is a software package for finding domains in protein sequences. ADDA has moved to github (https://github.com/AndreasHeger/adda)
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  • 5
    Prodar

    Prodar

    Prodar searches the PDB for candidate protein structural alignments

    Prodar is a search application that queries the PDB for candidate structural alignments. The input to the search is a protein backbone structure read from a standard (text) PDB file, and the results returned are based solely on structural similarity of the backbone without any regard to sequence information. Searches are extremely fast, searching the PDB (included in app) in less than a minute typically. Prodar identifies partial matches, such that a relatively small section of the query...
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  • 6
    alignlib is a C++ library for computing and manipulating sequence alignments of protein sequences. Most of the functions and classes are exported to python thus permitting easy scripting of complex tasks. Alignlib has moved to github (https://github.com/AndreasHeger/alignlib)
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  • 7

    HPeak

    A HMM-based algorithm for defining enriched regions from ChIP-seq data

    HPeak is a hidden Markov model-based approach that can accurately pinpoint regions to where significantly more sequence reads map. Testing on real data shows that these regions are indeed highly enriched by the right protein binding sites. Command (single-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -t TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -fmin 100 -fmax 300 -r 36 -ann -wig -seq -interfiles Command (pair-end): perl /compbio/software/HPeak3/HPeak.pl -sp...
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  • 8
    NeedlemanWunsch

    NeedlemanWunsch

    Fast global sequence alignment for the masses!

    MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/
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  • 9
    SmithWaterman

    SmithWaterman

    Fast local sequence alignment for the masses!

    MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/
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  • 10
    Software for making Clusters of Orthologous Groups (featuring the new EdgeSearch algorithm). Latest ref: Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A. Bioinformatics 2010.
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  • 11
    Tangerine is a protein sequence alignment tool based on cross-correlation. Its aim is to provide maximum sensitivity while being computationally efficient.
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  • 12
    This is a research-level program used to track protein translocation in live cell imaging experiments when the nucleus is not specifically marked by either stain or transfected fluorescent proteins.
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  • 13
    ProteinShop is an interactive protein manipulation tool. Users apply their knowledge and intuition to quickly create a set of protein configurations that can be subjected to local or global optimization. More information at http://proteinshop.org
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  • 14
    Robinviz
    Reliability Oriented Bioinformatic Networks Visualization
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  • 15
    Windows command line utility calculating protein orthologs using best reciprocal hit from BLAST alignment output
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  • 16
    Open Source project for visualizing protein structure. Written in C++ with Qt and OpenGL the software is designed to be multi-platform (Linux, FreeBSD and Windows). On web: www.msprot.com Copyright 2008 Federal University of Sao Paulo - UNIFESP
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  • 17
    C++ library for protein sequence profile to profile alignment. Implementing numerous known alignment variants in a flexible and manageable architecture.
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  • 18
    BigBang/Horizon is a proteomics data analysis pipeline with focus on the shotgun LC/MSMS workflow.
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  • 19
    The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!
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  • 20
    EMBOSS Suite
    EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
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  • 21
    Fast5 is a probabilistic file format for the storage of nucleotide and protein sequences based on hdf5.
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  • 22
    Software to cluster protein sequences into functionally similar groups. Journal reference: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/16/1765
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  • 23
    This project implements an algorithm for segmenting protein sequences into smaller meaningful blocks. The method is based on the pure statistical approach and it uses an analogy between proteins and natural language.
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  • 24
    Moleculizer is a tool for simulating and generating biochemical reaction networks that are specified through a set of rules for protein-protein interactions.
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  • 25
    RAINIER: Rapid Automated Inference of Nucleic-Acid Interaction Energy using Refinement RAINIER is a protein simulator that can predict the interface structure of DNA- and RNA-binding proteins, using statistical and physical techniques.
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