Search Results for "reference" - Page 9

TreQ aims at mapping reads from next generation sequencing (NGS) data to a reference genome, with emphasis on accuracy in the presence of structural variations like insertions and deletions.

This is an approach that complements previous methods for reliable homozygous structural variation identification. Our approach accurately determines genotype and breakpoints relative to a reference genome based on de novo assembly of Illumina Genome Analyzer sequencing data. In this method, we examined only homozygous structural variations because detecting heterozygous structural variations requires assembly of haplotype sequences, which is not yet possible using existing assemblers.

A very simple command line tool to convert OSM files to Shapefiles. Written in Java. Think of it as a self-study project.

The Blast2SNP is able to pick out synonymous, non-synonymous mutations and indels from draft assembly sequences by performing BLAST search against the reference ORF sequences.

Software for making Clusters of Orthologous Groups (featuring the new EdgeSearch algorithm). Latest ref: Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A. Bioinformatics 2010.

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.

fastqz is a compressor for the most common (Sanger format) FASTQ files produced by DNA sequencing machines. It may be used with a reference genome for better compression.

A plugin for JabRef. The plugin queries Zentralblatt MATH reference entries using the BibTeX format.

GeoPMS is a project based full paper management system to archive, search and manage scientific papers. GeoPMS has full text search, search by author, search by title and citation import functionality direct from the PDF header, PDF text or RIS. Reference list design can be selected for each project.

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. It has internal projects manageable and ability to export results in the standard formats of the area.

A python-based calculator that uses the Sabine, Norris-Eyring and Fitzroy formulae to calculate the RT60 time of a room with given specifications. Material list from SAE Institute reference.

The ETHNOS environment is composed of: 1) ETHNOS-6, a dedicated distributed real-time operating system (developed as an extension to Linux), from which the overall environment takes its name, supporting different high level representation, communication, and execution requirements, 2) a dedicated network protocol designed for both the single robot and the multi-robot environment, specifically designed for noisy wireless communication, 3) an object oriented Application Programming Interface (API) based on the C++ language (and a subset based on Java), 4) a set of additional development tools (a robot simulator, a Java-applet template, etc.). Check the official website for a Reference Manual.

A set of Unix command line tools for quick and convenient batch processing of tabular text files (a.k.a., tab-delimited, csv, or flat file format) with a header line. Provides delimiter and compression detection, column reference by name. * tblmap: per-line ("map") computation: derive columns through an expression, delete, reorder, filter rows. * tblred: compute ("reduce") aggregations (e.g., sum, average) over groups defined by key columns. * tbldesc: Summarize columns in file (e.g., proportion of character/numeric values, min/mean/median/max, missing values, correlation with a target column)...

It maps sequencing reads with MTB reference genome (H37Rv) using NCBI blast, and finds out mutation sites.

ArgooMap is an online, map-based discussion forum, which allows participants to reference their contributions to geographic locations. Different versions of ArguMap and ArgooMap/Argoomap were developed by students supervised by Dr. Claus Rinner at Ryerson University (Toronto, Canada) with partial funding from the GEOIDE Network of Centres of Excellence and DAAD, the German Academic Exchange Service. Past and current developers at Ryerson and the University of Muenster include: - Carsten Keßler - Marius Austerschulte - Sepehr Mavedati - Sami Munshi - Matrica Joshi Alternative versions (not yet available here) were developed by: - Aaron Sani (Ryerson) - Soheil Boroushaki (Univ. of Western Ontario) - Ana Simao (University College London) The ArgooMap Sourceforge project page contains two implementations of the package, which diverged from a single older version, ArguMap. ...

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.

This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted.

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.

A GUI program to create the plasmid database forms for BGME lab. This program presents user with a data entry form for entering plasmid information and automatically converts DNA sequence to protein, aligns it, and creates text output file.

SVGMap is an open source web tool to help you in the visualisation of experimental data associated to some graphical representation. More at : 1. Project website http://bg.upf.edu/svgmap 2. Reference : Xavier Rafael-Palou, Michael P. Schroeder, and Nuria Lopez-Bigas SVGMap: configurable image browser for experimental data Bioinformatics 2011 : btr581v1-btr581.

Fits and scores vertices from models onto reference vertices to find its polyhedral identity and symmetry quantitatively. Java based with GUI

An android app to display nutrient contents of basic food items, and to calculate nutrient contents of complex meals and menus of arbitrary periods compared to the Dietary Reference Intakes to analyze and refine diets. (Nutrika for Android)

The goal is to provide a desktop application to display nutrient contents of basic food items, and to calculate nutrient contents of complex meals and menus of arbitrary periods compared to the Dietary Reference Intakes to analyze and refine diets.

Ordering and Programming Gateway component developed by TELESPAZIO in the frame of ESA activities for providing a reference implementation of Candidate Standard OGC 06-141r6 Ordering Services For Earth Observation Products.

An R package that performs forward-backward fragment assembling segmentation. Reference: BMC Bioinformatics. 2007 May 3;8:145.