Discovering new genes with advanced homology detectionWeizhong Li
Quorex Pharmaceuticals, 1890 Rutherford Road, Suite 200, Carlsbad CA 92008, USA
Trends Biotechnol 20:315-6. 2002
..Alternative approaches involving more sensitive homology recognition methods are playing an increasingly important role in the next stage of gene discovery. The hunt for new genes is far from over...
- Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Weizhong Li
Burnham Institute for Medical Research La Jolla, CA 92037, USA
Bioinformatics 22:1658-9. 2006
..All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST...
- Tolerating some redundancy significantly speeds up clustering of large protein databases
Weizhong Li
The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
Bioinformatics 18:77-82. 2002
..Although some redundancy is present after clustering, our new program's results only differ from our previous program's by less than 0.4%...
Gene identification and protein classification in microbial metagenomic sequence data via incremental clusteringShibu Yooseph
J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
BMC Bioinformatics 9:182. 2008
..and consequently gene identification is challenging. The vast amount of sequence data also requires faster protein family classification tools...
- Crystal structure of the tetrameric inositol 1-phosphate phosphatase (TM1415) from the hyperthermophile, Thermotoga maritima
Kimberly A Stieglitz
Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
FEBS J 274:2461-9. 2007
..Two of the subunits have the active site loop folded into a beta-hairpin structure, whereas in the remaining two subunits the same loop adopts an alpha-helical conformation...
- VISSA: a program to visualize structural features from structure sequence alignment
Weizhong Li
Burnham Institute for Medical Research, La Jolla, CA 92037, USA
Bioinformatics 22:887-8. 2006
..This program, called Visualize Structure Sequence Alignment, also has many other built-in tools that can help analyze multiple sequence alignments. AVAILABILITY: http://bioinformatics.burnham.org/liwz/vissa CONTACT: liwz@burnham.org...
- FFAS03: a server for profile--profile sequence alignments
Lukasz Jaroszewski
Bioinformatics Program, The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
Nucleic Acids Res 33:W284-8. 2005
..Access to the server is open for both academic and commercial researchers. The FFAS03 server is available at http://ffas.burnham.org...
- Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate
Andrew Y Gracey
School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L39 7ZB, United Kindgom
Proc Natl Acad Sci U S A 101:16970-5. 2004
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- A segment alignment approach to protein comparison
Yuzhen Ye
The Burnham Institute, La Jolla, CA 92037, USA
Bioinformatics 19:742-9. 2003
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- Sequence clustering strategies improve remote homology recognitions while reducing search times
Weizhong Li
The Burnham Institute, La Jolla, CA 92037, USA
Protein Eng 15:643-9. 2002
..All methods are evaluated with a large fold-recognition benchmark...
- Cloning and characterization of glucose transporter 11, a novel sugar transporter that is alternatively spliced in various tissues
Xiaohua Wu
The Burnham Institute, La Jolla, CA 92037, USA
Mol Genet Metab 76:37-45. 2002
..Furthermore, a liposome reconstitution functional assay showed that GLUT11-L has glucose transport activity...
- In search for more accurate alignments in the twilight zone
Lukasz Jaroszewski
Program in Bioinformatics and Biological Complexity, The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
Protein Sci 11:1702-13. 2002
..We combined their best features and produced a hybrid method, which yielded alignments that surpassed the original alignments for about 50% of protein pairs with minimal computational effort...
- Probing metagenomics by rapid cluster analysis of very large datasets
Weizhong Li
California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, California, USA
PLoS ONE 3:e3375. 2008
..2007 PLoS Biol 5, e16). Such datasets, not only by their sheer size, but also by many other features, defy conventional analysis and annotation methods...
