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As products of scientific research, we publish articles in journals and present findings in conferences.
We also try our best to make software tools and database available to the research communities, most of
which are web-accessible and free for academic use.
We appreciate proper acknowledgments and citations.
Some of the tools and database might require the application of a license.
Copyright Notice.
The documents contained in this directory are included by the contributing authors as a means to
ensure timely dissemination of scholarly and technical work on a non-commercial basis.
Copyright and all rights therein are maintained by the authors or by other copyright holders, notwithstanding
that they have offered their works here electronically.
It is understood that all persons copying this information will adhere to the terms and constraints invoked by
each author's copyright.
These works may not be reposted without the explicit permission of the copyright holder(s).
- COPredictor (2007)
calculates and/or predicts the absolute contact order (CO) for a given protein sequence.
Given an input protein sequence, COPredictor will first use BLAST to identify sequences that are either identical or homologous to
those in our CO database.
There are three possible scenarios:
1) If the input sequence exactly matches a known structure in our database (or the input is a 3D structure), COPredictor will
calculate its CO directly using a formula[5];
2) If the BLAST search finds a homolog that is not an exact match to the input sequence but satisfies certain criteria,
the pre-computed CO of the homologue is used as the predicted CO of the query sequence;
3) If the input sequence has no BLAST match that falls into the second scenario, COPredictor will call Proteus to predict
the secondary structure content for the query protein, and then report its CO using another formula[5].
Average calculation times are around 35 seconds for the CO calculator and about 27 seconds for the CO predictor.
[5]
Y. Shi, J. Zhou, D. Arndt, D. S. Wishart, and G. Lin.
"Protein Contact Order Prediction from Primary Sequences".
BMC Bioinformatics.
9(2008): 255.
- SNPLink (2006-2007)
deterministically identifies the chromosomal regions shared by family members, using the
high density SNP genotype data. The current version handles (only) "tree pedigrees", with either one
or both grandparents (extension to more general cases is undergoing). With disease information for members
provided, SNPLink unambiguously locates their shared chromosomal region(s), where the responsible
gene(s) might reside.
Its version 2.0 (for Windows and Linux) was released on July 3, 2007[4].
[4]
G. Lin, Z. Wang, L. Wang, Y.-L. Lau, and W. Yang.
"Identification of Linked Regions Using High-Density SNP Genotype Data for Linkage Analyses".
Bioinformatics. 24(1)(2008), 86-93.
- PSAtip (2002-2006)
is a program for protein NMR backbone resonance sequential assignment, with the input being
spin systems (ideally containing HN, N, CA, CB chemical shifts). PSAtip solves the assignment
optimally through integer programming via a call to Cplex.
Its version 1.1 was released on April 27, 2006.
- Rnall (2004-2005)
predicts the local secondary structure energy landscape for an RNA sequence[3].
It could be useful in locating genes in a genomic sequence.
[3]
X.-F. Wan, G. Lin, and D. Xu.
"Rnall: An Efficient Algorithm for Predicting RNA Local Secondary Structural Landscape in Genomes".
Journal of Bioinformatics and Computational Biology, 4(5)(2006), 1015-1031.
- RNA Align (2000-2001)
computes an alignment for two RNA secondary structures based on the model and the
algorithm presented in Lin et al. (2001)[1] and described in full details
in Jiang et al. (2002)[2].
Note that this is an obsolete version and a better version can be found at Dr. Kaizhong Zhang's website.
[2]
T. Jiang, G. Lin, B. Ma, and K. Zhang.
"A General Edit Distance between RNA Structures".
Journal of Computational Biology. 9(2)(2002), 371-388.
[1]
G. Lin, B. Ma, and K. Zhang.
"Edit Distance between Two RNA Structures".
In ACM RECOMB 2001, pages 211-220.
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