Amarendran R. Subramanian

TL;DR: DIALIGN-TX is presented, a substantial improvement of DIAL IGN-T that combines the previous greedy algorithm with a progressive alignment approach and produces significantly better alignments, especially on globally related sequences, without increasing the CPU time and memory consumption exceedingly.

TL;DR: A complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN and is comparable to the standard global aligner CLUSTAL W, though it is outperformed by some newly developed programs that focus on global alignment.

TL;DR: The maximal and maximum cliques problem arises naturally in DNA sequence analysis where the maximal cliques might be interpreted as functional domains carrying biologically meaningful information and it is proved that the recognition problem for max-tolerance graphs is NP-hard.

TL;DR: A semi-automatic approach to multiple sequence alignment where biological expert knowledge can be used to influence the alignment procedure and produce alignments that reflect the true biological relationships among the input sequences more accurately than fully automated procedures can do.

TL;DR: This work introduces web interfaces for two recent extensions of the multiple-alignment program DIALIGN and offers a version of DIAL IGN that uses predicted protein secondary structures together with primary sequence information to construct multiple protein alignments.