Search Results for "genome" - Page 3

iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/). iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in text format and provides results in genome track formats (BED and GFF3 files), which can be easily imported into genome browsers. For more details about iPiG and it's functionallity, please see "iPiG: Integrating Peptide Spectrum Matches Into Genome Browser Visualizations" Mathias Kuhring and Bernhard Y. ...

An integrated bioinformatics toolkit for analysis of ChIPseq data from the Illumina DNA sequencing platform. Includes filtering, quality control, simulation, peakfinding, visualization, and comparison of samples.

...This behavior is controlled by a genetically evolved neural net augmented with online back propagation learning. The back propagation learning uses a reward vector and plasticity matrix that is evolved as part of the genome. Long story short, the AI is pretty frickin' sophisticated. Players can take control of organisms, trade resources and organisms in a market, and aid evolution by selective breeding.

...Research paper publication: http://www.bioinformation.net/008/97320630008365.htm BatchPD checks specificity via in-silico PCR, provide gene/exon specific relevant information summarised in an end spread-sheet; Primer design, PCR checks and other relevant information are queried from existing online tools with BatchPD acting as an intermediate to handle queries and results processing. BatchPD interfaces with the following online bioinformatic resources: * NCBI's GenBank * USCS's Genome browser * ExonPrimer Optional extra SNP checks can be carried out via the web tool: SNPCheck. BatchPD Uses the HtmlCleaner package: http://htmlcleaner.sourceforge.net/

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.

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.

The Celera Genome Browser, developed at Celera Genomics as part of Celera's sequencing and annotation of the human genome, and released as open source in 2006.

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.

A computational tool to design and annotate metabolic pathways from genome annotations

Blast2KEGG provides an approach mapping predicted genes to pathways by their annotations, then draw on KEGG maps. It performs fuzzy matching from enzyme name to EC number. There are annotation editor and genome broswer integrated in this application.

CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.

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.

CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74

A new host of CpG Island Explorer 2.0. Original article: An evaluation of new criteria for CpG islands in the human genome as gene markers, Yong Wang on Bioinformatics 2004. http://bioinformatics.oxfordjournals.org/content/20/7/1170.abstract

A Java application used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.

This program serves to provide any useful information regarding a set of loci on the genome. For every genomic position provided, the Annotater will return any "known" information regarding that position.

Technology sandbox for the knowledge genome project

A system based on the multiagent approach, to help the biologists with the manual annotation task on genome sequencing projects

DraGnET is designed to assist with the management of annotated draft and complete genome sequence data. DraGnET also provides a web interface for BLAST and Batch BLAST search capabilities. Each search page has instructions for the use of the page.

...Users can combine tools in automatic analysis workflows, which can be shared. Chipster's interactive visualizations allow users to select datapoints and create new gene lists. For NGS data Chipster contains a built-in genome browser, which highlights SNPs and automatically indexes BAM files and calculates coverage. Chipster’s ability to provide a biologist-friendly access to a powerful analysis platform is technically based on a desktop application user interface, a flexible distributed architecture, and the ability to integrate many types of analysis tools (command line, R/Bioconductor, Java, Web Services etc). ...

OmicBrowse, developed with Flash and Java, is a highly evaluated genome browser integrating omics knowledge ranging from genomes to phenomes and is especially appropriate for positional-cloning purposes.

ARTADE (ARabidopsis Tiling-Array-based Detection of Exons) is a standard tool for the automatic annotation of genome-wide tiling-array data in Arabidopsis. ARTADE is a program originally written by Dr. Tetsuro Toyoda, RIKEN, Japan.

This is a small and easy-to-use bio informatics tool for rookie and expert biologists to split files which contain sequences (these files can contain nucleotide, genome or protein sequences) into individual ' .fasta ' files.

RepeatMap is a collection of time/memory efficient algorithms and data structures to enable rapid counting & querying of kmers (sequences of length k) counts in large sequences. E.g. a query could be "how many times is 'ACGTCATGGTAC' found in a genome."

...Applied Biosystems SeqScape, Paracel Genome Assembler, MTexpert, etc.).