Search Results for "sequence scaffold, java" - Page 7
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Showing 213 open source projects for "sequence scaffold, java"
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The Antigen Variability ANAlyzer (AVANA) tool uses information entropy to measure variability in protein sequence alignments. It also compares alignments using mutual information, identifying the mutations that characterize specific sequence sets.
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BACContigEditor is a simple sequence alignment editing tool, written in Java. It is originally developed for finishing BAC shotgun sequencing projects, but the program could be easily extended to the whole genome project.
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A bioinformatics package to analyse ESTs (Expressed Sequence Tags) easily. It contains functionalities of ESTs for EST submission, Batch BLAST and BLAST result parser, etc. easiEST contains JAVA GUI applications for analysing ESTs or other sequences
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DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV
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prot3d is aimed to get three-dimensional folding possibilities of a peptide given its aminoacid sequence.
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DUPS can be used to present any set of images depicting a chronological sequence. It creates a set of HTML pages acting as a browser based picture/pdf viewer. The emphasis lies on displaying two pictures side by side enabling the user to compare them.
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With this tool a single image or a sequence of images can be transformed into a Super Overlay for Google Earth.
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JRET (Java Reverse-Engineering Tool) is a program that is capable of reconstructing sequence diagrams from JUnit testsuites through dynamic analysis. It is written in Java/AspectJ and provides a GUI as well as command-line possibilities.
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Sipana is a distributed SIP monitoring tool to monitor the SIP signaling behavior using sequence diagrams and providing SIP end-to-end performance metrics through a centralized Web interface. For more information please visit http://sipana.org/
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Re-searcher is the system for recurrent psiblast searches. It enables timely detection of new proteins on the protein sequence databases. Searches can be done on a local server or at NCBI. It has a user-friendly web interface.
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PepT-IDE is a protein analysis tool that is used for multiple sequence alignment, 3D visualization and displaying protein contact maps for protein sequences and structures. It also has feedback communication between the different views of the protein.
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Java application that puts up a dialog and allows one to modify the overall volume levels of a MIDI file. Also trims leading and trailing silent regions. Volume can be adjusted while the MIDI sequence is playing.
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ORFer reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. ORFprimer is an extended software package for high throughput PCR primer design for biological sequences
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Geneview is a visualisation tool to display genetic sequence data stored in nucleic sequence databases like <A HREF="http://www.ncbi.nlm.nih.gov/Genbank/">GenBank</A>.
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J3dPSV 1.0 is a graphical application package for viewing and modeling of three dimensional structures of protein structure, including multiple chain sequence table and a three-dimensional (3D) protein structure viewer.
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Many design artifacts can be directly executed. UML state processes can be executed by a state machine; UML sequence diagrams can be executed directly. ExecDesign will be a suite of Java tools which can be used to document and execute UML designs.
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BioStream enables bioinformatics researchers to create, query and apply tools to their own databases. It supports sequence files and other data types by allowing the creation of metadata definition files.
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OpenTimeLine is a project to provide to the community a framework and a new kind of Music sequencer dedicated to graphical scores. It use the fudi protocol to sequence events for Pure Data.
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JSequencer is a development tool which autogenerates Sequence diagrams. It's ideal for design and debugging. Wire it with Spring and you can produce Sequence Diagrams without writing any code! The produced output can be viewed using SequencerUI(included
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BIOLAP - OLAP for Genome and Biology Data Sets. This project extends Mondrian OLAP to biology data sets. We provide tools to slice and dice genomic sequence similarities and more easily explore large genomic data sets.
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PARs is a bioinformatics tool for the analysis of cis-regulatory DNA sequences. Composed of two parts: a suite of sequence analysis algorithms for predicting cis-binding sites in DNA sequences and a GUI for visualisation and exploration of the results.
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Framework that adds security functions to Java web applications. It is used as an add-on for Struts framework. It is written in Java and provides web-commands for java web pages and provides several security services such as sequence control invocation.
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DNA Replicator is a graphical tool (written in java) that compute the complementary sequence from an input DNA sequence. It's a really easy used application.
