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Literature DB >> 1631095

Parametric sequence comparisons.

Abstract

Current algorithms can find optimal alignments of two nucleic acid or protein sequences, often by using dynamic programming. While the choice of algorithm penalty parameters greatly influences the quality of the resulting alignments, this choice has been done in an ad hoc manner. In this work, we present an algorithm to efficiently find the optimal alignments for all choices of the penalty parameters. It is then possible to systematically explore these alignments for those with the most biological or statistical interest. Several examples illustrate the method.

Mesh：

Year: 1992 PMID： 1631095 PMCID： PMC49443 DOI： 10.1073/pnas.89.13.6090

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

14 in total

9. A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations.

Authors: G A Komatsoulis; M S Waterman
Journal: Appl Environ Microbiol Date: 1997-06 Impact factor: 4.792

10. Optimizing substitution matrix choice and gap parameters for sequence alignment.

Authors: Robert C Edgar
Journal: BMC Bioinformatics Date: 2009-12-02 Impact factor: 3.169

Parametric sequence comparisons.

1. A local algorithm for DNA sequence alignment with inversions.

2. Optimal sequence alignments.

3. Optimal sequence alignment allowing for long gaps.

4. Rapid and sensitive protein similarity searches.

5. A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons.

6. Evaluation and improvements in the automatic alignment of protein sequences.

7. A general method applicable to the search for similarities in the amino acid sequence of two proteins.

8. An improved algorithm for matching biological sequences.

9. Rapid similarity searches of nucleic acid and protein data banks.

10. Simian sarcoma virus onc gene, v-sis, is derived from the gene (or genes) encoding a platelet-derived growth factor.

1. In search for more accurate alignments in the twilight zone.

2. Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data.

3. Template-based protein structure modeling using TASSER(VMT.).

4. Tropical geometry of statistical models.

5. Parametric inference for biological sequence analysis.

6. A code for transcription initiation in mammalian genomes.

7. Protein structure prediction by pro-Sp3-TASSER.

8. Uncertainty in homology inferences: assessing and improving genomic sequence alignment.

9. A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations.

10. Optimizing substitution matrix choice and gap parameters for sequence alignment.