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XGI :: X Genome Initiative
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"There is measure in all things. There are fixed limits beyond
which and short of which right cannot find a resting place."
-- Horace, Satires
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| ABSTRACT |
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The X Genome Initiative (XGI) is a comprehensive integrated system for the storage, analysis and visualization of DNA sequences. It was designed as a solution for high throughput expressed sequence tag (EST) and genomic sequencing operations that require professional bioinformatics support, either operating remotely or in-house.
The system is typically run in "remote" mode, wherein the database and pipeline software are housed behind a secure firewall at NCGR, and is accessed by customers through http or encrypted https. The system can also be installed locally behind a client's firewall. The XGI System contains sophisticated security features that permit selective sharing of data among different user groups operating in either mode.
XGI assists researchers by automating a long series of sequence processing and analysis operations, and organizing the sequences and results of their analysis in a way that is intuitive for biologically-oriented scientists.
Researchers deposit sequences at NCGR over the Internet or by using media such as CD, the analysis pipeline is applied to these sequences and after a short processing period, users are able to explore the sequences and the analytical results of the pipeline operations over the World Wide Web (WWW).
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| COMPONENTS |
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The XGI software software system is comprised of three components:
- An automated sequence analysis pipeline
- Relational database
- A web-based interface for search and view operations
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| ARCHITECTURE |
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The core data element in XGI is the nucleotide sequence. All features and annotations are decorations on nucleotide sequence. Raw sequences are input into the system and undergo a screening process to remove contamination and low quality reads before being accessioned into the database in their mature form. Subsequent analysis steps are performed on mature sequences.
XGI employs a web-based search functionality that enables sequence searching from multiple entry points (through annotation, analysis results, sequence names etc.), allows one to save the results of searches for later use, and export sets of sequences in FASTA and raw text format. In EST pipeline mode, XGI employs clustering to reduce sets of expressed sequence tags into more useful and stable gene sequences- consensus sequences derived from EST clusters. All subsequent analysis operations are performed on consensus sequences, which reduces computational and interpretational complexity.
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| XGI DOWNLOAD |
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XGI is freely available to the academic community and non-profits. If you have an account, download XGI directly from our server. If you do not have an account, we request that you first create an account. A secure customized XGI can be set up for you and run at NCGR with encrypted web access. Alternatively, the entire system can be
configured and installed at your location.
If you have further questions about XGI or are interested in deploying a local version of XGI for commercial purposes, please contact us at xgi-feedback@ncgr.org.
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| CONTACT |
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Kamal Gajendran
National Center for Genome Resources
2935 Rodeo Park Drive East
Santa Fe, New Mexico 87505
USA
(phone)
+1 505 995 4409
+1 800 450 4854
(fax)
+1 505 995 4432
(email)
xgi-feedback@ncgr.org
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