Search Results for "alignment" - Page 18

SOCS performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences. Modes are available for detecting short sequence-space variants (such as SNPs) and for detecting unlimited numbers of bisulfite-induced nucleotide substitutions for 5mC methylation studies.

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.

This software implements a novel algorithm for alignment of PPI networks

KADMOS provides a lightweight API for alignment of OWL 2 ontologies. It is based on the OWL API v3.

FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.

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

Fast Unsupervised Sentence Aligner described in "Improved unsupervised sentence alignment for symmetrical and asymmetrical parallel corpora", COLING 2010. NEWS : release 1.0b : bug fixed (release1.0a deprecated).

gfmessage is a gtk2 based on screen message displayer which prints formatted text on screen. The text can be formatted either using format options such like font , alignment or color options or using the PANGO markup language in input text.

MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.

See Wiki page for details.

ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.

Mass Spectrometry analysis Pipeline

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.

BFAST facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance.

SolSNP is a Java-based DNA variant calling tool for Next-Generation Sequencing alignment data. SolSNP uses a modified Kolmogorov-Smirnov statistic and data filtering to confidently and quickly call variants on high-coverage aligned genomes.

Extract and append variables in parallel from a NetCDF file. Uses combine-batched asynchronous I/O with Parallel-NetCDF 1.2. Arena memory is managed to prevent swapping and fragmentation. Allows header padding, variable alignment and 64bit format.

Endian-Mode Switch tool for general purpose for Linux OS.

Bioinformatics Perl extension for the analysis of antibody variable domain repertoires. Suitable for mammalian repertoire sequences obtained either by Sanger or 454 sequencing. Methods published in Glanville, Zhai, Berka et al, PNAS 2009.

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

This Java software permits to control a real robot over a WiFi connection from one or more desktop client. Built in support for Pololu, Phidgets, SparkFun and any RS232 device. You can build and run your own robot by just editing a simple config file

We will develop a Sequence alignment LIMS System to integrate multiple NGS(Next Generation Sequencing) System. The system will be developed, based on EJB technologies.

Construct a board string on multiple lines with labels values possibilities with basic alignment

...The framework includes mixins, modifier classes, and responsive breakpoints so layouts adapt fluidly across screen sizes. By starting with a consistent baseline, Blueprint CSS reduces cross-browser quirks and gives designers confidence in spacing, proportion, and element alignment. Teams often use it as the “CSS backbone” of internal tools, web products, or component libraries.

Built around LDC's champollion sentence aligner kernel, Champollion Tool Kit (CTK) aims to providing ready-to-use parallel text sentence alignment tools for as many language pairs as possible.

Protein ALignment Optimiser (PALO) is a script for the selection and alignment of the best combination of transcripts among orthologous genes. PALO is mainly written in Python, although other programming languages are also implemented (R, Perl...).