Designing seeds for similarity search in genomic DNA
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds
BIBE '04 Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering
Optimizing Multiple Seeds for Protein Homology Search
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Optimal spaced seeds for hidden Markov models, with application to homologous coding regions
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
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Pair-wise sequence alignment is the basic method of comparative analysis of proteins and nucleic acids. Studying the results of the alignment one has to consider two questions: (1) did the program find all the interesting similarities ("sensitivity") and (2) are all the found similarities interesting ("selectivity"). Definitely, one has to specify, what alignments are considered as the interesting ones. Analogous questions can be addressed to each of the obtained alignments: (3) which part of the aligned positions are aligned correctly ("confidence") and (4) does alignment contain all pairs of the corresponding positions of compared sequences ("accuracy"). Naturally, the answer on the questions depends on the definition of the correct alignment. The presentation addresses the above two pairs of questions that are extremely important in interpreting of the results of sequence comparison.