Search Results for "sequence scaffold, java" - Page 5
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Showing 111 open source projects for "sequence scaffold, java"
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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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Calculates the shape of a telescope mirror from a sequence of Foucault test images. Java-based GUI simplifies entering and organizing measurement data. Logging and comparison functions enable quantification of the effects of various figuring strokes.
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Java Chaotic Random Number Generator - Inspired by chaos theory, the intent of this generator is to produce unseeded, unpredictable numbers. The numbers will not follow a predictable sequence and will not rely on a pseudorandom algorithm.
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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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Given a String , returns the next logically sequential string defined by a rule. The basic rule is, given a sequence of alphabets, it checks the string and returns a new string with one or more alteration. javadocs and source codes available inside.
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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
