Search Results for "alignment" - Page 2

JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences.

Alignment Based Learning 4 Java is a port of ABL 1.1.

Alignment of the assembled sequences to a reference genome is a common way to obtain a likely order for the contigs, though most of times the final decision is taken by the user. We present the jContigSort, a tool that sorts the genome contigs.

Distributed phrase-based machine translation training tool based on Hadoop.

MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.

3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.

SRMA is a post-alignment micro re-aligner for next-generation high throughput sequencing data.

This is a pipeline that is used to store an EST or Genome assembly information including reads and their alignment in a mysql database. Further more, it provides a set of scripts to mine SNPs and other statistics from the assembly.

Sanchay is a collection of tools and APIs for language researchers. It has some implementations of NLP algorithms, some flexible APIs, several user friendly annotation interfaces and Sanchay Query Language for language resources.

ZAE is a Zoomable multiple sequence Alignment Editor

LaJolla can perform 3D alignments of RNA and protein structures. It is fast, simple to use and well tested. LaJolla is successfully published in a peer reviewed journal. !!!!!! PROJECT MOVED TO GITHUB !!!!!! Please check out http://raphaelbauer.github.io/lajolla/

AlViz is a research prototype for visual ontology alignment implemented as multiple-view plug-in for Protege using J-Trees and Graphs. Based on similarity measures of an ontology matching algorithm AlViz helps to assess and optimize the alignment results

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.

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.

A tool to compare two Protein Sequences and show similarities with the help of dotplot.

Spectre for mass spectrometry. (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data. (working on mzDATA). Provides filters, alignment- and export tools.

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.

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.

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.

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.

ANNALIST (Annotation, Alignment and Scoring Tool) is a scoring tool for the evaluation of the output of text-based semantic annotation systems.

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.

A bi-directional BLAST tool for orthologue listing with extended facilities (global alignment; paralogue list; GO onthology; dN/dS; etc) working on Win32 compiled versions of NCBI BLAST,FASTA,EMBOSS, and PAML. FILES AVAILABLE AT THE HOMEPAGE.(JAVA coded)