Search Results for "sequence scaffold, java" - Page 4
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Showing 92 open source projects for "sequence scaffold, java"
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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.
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TaxonDNA is a simple but extensible system for performing simple DNA (and other) sequence manipulations in Java. We hope to create a simple framework which can be quickly extended to create bioinformatics applications.
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PROMPT is a system for retrieval, analysis, mapping and comparison of proteins. It allows easy mapping of different types of sequence IDs, data retrieval and integration, a multitude of analysis and comparison algorithms and a full-blown easy to use GUI.
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StatGen uses information from a genetic distance matrix or a newick tree to summarize the sequence variation within or between groups of sequences with summary statistics and produce graphical reports of those statistics.
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Tools for comparative sequence analysis. Includes FamilyRelations (GUI) and a C++ toolkit/Python wrapper for doing fixed-width-window analyses.
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A Mass Spectrometer B and Y ion labeling software for proteomics researchers. Peptide sequences can be read from a library and b and y ions will be calculated and sequence can be manipulated by the user (chem. mod. or amino acid mod.)
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ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster data sets.
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LineageEvolver is a simulation system for molecular evolution. Sequence evolution is simulated using modular processes such as substitutions, gene duplication/death, horizontal gene transfer, and more.
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DNAGalaxy is an attempt to produce an open-source bioinformatics software alternative to the expensive DNAStar Lasergene software. Its features currently include Blast and Entrez searching, a frontend to clustal and a sequence editor. It requires java1.5
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JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model.
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GATA is a graphic alignment tool for comparative sequence analysis. It makes use of BLAST to graphically align two DNA sequences, creating box- line- box representations of window scored local alignments. GATA also displays extensive GFF gene annotation.
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Sequence studio main package provides classes and interfaces for various kinds of sequence alignment. Differently from regular expressions it computes similarity with two initially unknown strings. Project page provides code generating applet.
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NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.
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MARSHAL (Managing Additional References in Short-Read Alignment) enables short-read nucleotide sequence aligners to simultaneously analyze multiple references, facilitating the detection of structural variation.
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danaides
Meta data extractor based on ontologies
Danaides stores meta-data from biological banks in a graph databases as well as OBO formatted ontologies. It also provides a web query interface to parse ontologies or extract nodes based on ontology requirements. Example: Get all known elements that are in family of Fish (species ontology) AND a RNA (sequence ontology). -
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PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management.Statistical validation, , visualization, and converters from raw MS data open mzXML mzData format
