Document Detail


SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer.
MedLine Citation:
PMID:  22419785     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
SUMMARY: Existing SAM visualization tools like 'samtools tview' (Li et al., 2009) are limited to a small region of the genome, and tools like Tablet (Milne et al., 2010) are limited to a relatively small number of reads and may fail outright on large datasets. We need to visualize complex ChIP-Seq and RNA-Seq features such as polarity as well as coverage across whole 3 Gbp genomes such as Human. We have addressed these problems in a lightweight visualization system called SAMSCOPE accelerated by OpenGL. The extensive pre-processing and fast OpenGL interface of SAMSCOPE provides instantaneous and intuitive browsing of complex data at all levels of detail across multiple experiments.
AVAILABILITY AND IMPLEMENTATION: The SAMSCOPE software, implemented in C++ for Linux, with source code, binary packages and documentation are freely available from http://samscope.dna.bio.keio.ac.jp.
Authors:
Kris Popendorf; Yasubumi Sakakibara
Related Documents :
7487815 - Use of a spreadsheet program for circadian analysis of biological/physiological data.
23286135 - Dominant component analysis of electrophysiological connectivity networks.
22720685 - Cytoskeletal organization: whirling to the beat.
5132945 - A mathematical model of the human menstrual cycle.
21506765 - Tapeworms (cestoda: caryophyllidea), parasites of clarias batrachus (pisces: siluriform...
17521075 - Three-dimensional touch interface for medical education.
Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2012-03-13
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  28     ISSN:  1367-4811     ISO Abbreviation:  Bioinformatics     Publication Date:  2012 May 
Date Detail:
Created Date:  2012-04-30     Completed Date:  2012-12-07     Revised Date:  2014-07-31    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  England    
Other Details:
Languages:  eng     Pagination:  1276-7     Citation Subset:  IM    
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:
Animals
Bacillus subtilis / genetics
Computer Graphics*
Genome
Humans
Programming Languages
Sequence Alignment / methods*
Sequence Analysis, DNA / methods*
Software*

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


Previous Document:  Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data.
Next Document:  Fulcrum: condensing redundant reads from high-throughput sequencing studies.