Search Results for "k-meleon"

A command-line utility to manipulate biological sequences from a FASTA or FASTQ file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only. Compressed sequences files are supported if readable by zcat.

PWMScan is used to scan a position weight matrix (PWM) against a genome or, in general, a large set of DNA sequences. The PWM is the most commonly used mathematical model to describe the DNA binding specificity of a transcription factor (TF). A PWM contains scores for each base at each position of the binding site. The TF binding score for a given k-mer sequence is then obtained by simply adding up the base-specific scores at respective positions of the binding site. PWMScan takes as input...

---------------------------------------- IMPORTANT: Meraculous-2D has been superseded by the HipMer assembler, available here: https://sourceforge.net/projects/hipmer/ ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Efficient k-mer counting and deBruijn graph traversal - Two modes of handling of diploid allelic...

Complete new web project from me from 2014 realizing a youtube video downloader inclusive mp3 converting process. The project is coded in php, perl, jquery, ajax and css3. the web design is simple, but you can use it to set up new content. i dont publish the songtext content, but i give you all 30 perl created crawlers that extract content from lyrics and songtext webpages via wget. perl crawlers will then parse out the songtext content out of it. (c) Copyright: 2014 Sebastian...

BamBam includes numerous tools for analyzing DNA next-generation sequencing data. Tools are provided for calling SNPs and indels, identifying large scale deletions, tabulating counts of mapped reads, methylation analysis, and more. Depends on SAMtools (http://samtools.sourceforge.net/) and BAMtools (https://github.com/pezmaster31/bamtools). Also uses BioPerl, which is included in the download tarball.

Statistics modules in Perl Data Language, with a quick-start guide for non-PDL people. They make the PDL shell work like R, but with PDL threading (fast automatic iteration) of procedures including t-test, linear regression, and k-means clustering.

parastructure is a perl script collection to run the population genetics software STRUCTURE from Pritchard et al. 2000 (http://pritch.bsd.uchicago.edu/structure.html) in parallel on a cluster (beowulf type). Each run of K (the number of populations) is executed separately on each CPU of the cluster trough queue system based on PBS. A summary statistics table and distruct figures (Noah Rosenberg: http://www.stanford.edu/group/rosenberglab/distruct.html) are built at the end of the run. A patch...

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.

This is the high throughput PCR primer design software that is used at the J. Craig Venter Institute. See: Li K, et al. "Novel computational methods for increasing PCR primer design effectiveness in directed sequencing". BMC Bioinformatics 2008, 9:191.

Basic implementation of K-nearest neighbour Algorithm and the application of KNN to classify protein sequences as transmembrane beta barrel or non-transmembrane beta barrel on the basis of whole sequence amino acid composition given as input.

Human Configurator for iptables and tc [traffic control], in order to obtain a traffic-shaping system with a few of click. Basically, it's a perl script which parse an xml config file, where you can put your shaping and filtering rules for your net(s)/h

A CGI chatroom that is relatively small in size but does not skimp on the features.

AUC for Education is an GPLed intranet system designed for use in a K-12 setting that provides a web-based environment for students and teachers to interact via "Interactive Classrooms" and other innovative features.

The metaspace server is an object store that handles three things: encryption, version control and metatagging. Files stored in it will be searchable based on the metatags, and downloaded by anyone – although that will be useless without the encryption k

MyPHPSchool, intends to provide, modular and easy to modify content managment system specialized for K-12 Schools written in PHP, and using a MySQL database. Other Features include a Calendar, a Web Based Gradebook, and Remote File Acess for users.

The Shadow netWorkspace (SNS) is a web-based work environment designed to support learning, collaboration and communication in K-12 schools and higher education institutions.

Kwiki::Formatter::Textile is a Kwiki plugin providing Textile notation for the formatting of pages.