Learning Scoring Schemes for Sequence Alignment from Partial Examples
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Pair HMM based gap statistics for re-evaluation of indels in alignments with affine gap penalties
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Modeling conformation of protein loops by Bayesian network
LSMS/ICSEE'10 Proceedings of the 2010 international conference on Life system modeling and simulation and intelligent computing, and 2010 international conference on Intelligent computing for sustainable energy and environment: Part III
Computational Biology and Chemistry
Smolign: A Spatial Motifs-Based Protein Multiple Structural Alignment Method
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Touring Protein Space with Matt
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Formatt: correcting protein multiple structural alignments by sequence peeking
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
CONTRAlign: discriminative training for protein sequence alignment
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
A Knowledge-Based Multiple-Sequence Alignment Algorithm
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Summary: The Sequence Alignment Benchmark (SABmark) provides sets of multiple alignment problems derived from the SCOP classification. These sets, Twilight Zone and Superfamilies, both cover the entire known fold space using sequences with very low to low, and low to intermediate similarity, respectively. In addition, each set has an alternate version in which unalignable but apparently similar sequences are added to each problem. Availability: SABmark is available from http://bioinformatics.vub.ac.be Contact: ivwalle@vub.ac.be