A new approach to sequence comparison: Normalized sequence alignment

Bioinformatics

Volumn 17, Issue 4, 2001, Pages 327-337

  Arslan, Abdullah N ^a   Eǧecioǧlu, Ömer ^a   Pevzner, Pavel A ^b  

^a University of California at Santa Barbara   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC PROCEDURES; GENETIC VARIABILITY; MOLECULAR BIOLOGY; MOSAICISM; PREDICTION; PRIORITY JOURNAL; SCORING SYSTEM; SEQUENCE ANALYSIS; TIME;

EID: 0035021688     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/17.4.327     Document Type: Article

References (35)

1. Normalized local alignment improves the functional characterization of proteins
2. Statistical significance of ungapped alignments
3. Locally optimal subalignments using nonlinear similarity functions
4. Significance levels for biological sequence comparison using nonlinear similarity functions
5. Gapped Blast and Psi-Blast: A new generation of protein database search programs
6. The Erdös-Renyi law in distribution, for coin tossing and sequence matching
7. An efficient uniform-cost normalized edit distance algorithm
8. Efficient algorithms for normalized edit distance
9. The conserved exon method for gene finding
10. Comparative analysis of mouse and human DNA and applications to exon prediction
11. PairWise and SearchWise: Finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames
12. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
13. On nonlinear fractional programming
14. Parallel algorithms for fast computation of normalized edit distances
15. Gene recognition via spliced sequence alignment
16. Pattern recognition in nucleic acid sequences. i. a general method for finding local homologies and symmetries
17. Parametric recomputing in alignment graph
18. Computation of normalized edit distances and applications
19. Combinatorial optimization with rational objective functions
20. Prediction of the exon-intron structure by comparison sequences
21. The normalized string editing problem revisited
22. A dictionary based approach for gene annotation
23. Comparison of methods for searching protein sequence databases
24. Pipmaker-a web server for aligning two genomic DNA sequences
25. Pattern recognition in genetic sequences by mismatch density
26. Sensitivity and selectivity in protein similarity searches: A comparison of Smith-Waterman in hardware to blast and fasta
27. The identification of common molecular subsequences
28. Fast computation of normalized edit distances
29. Multiple hypothesis testing for sequence comparison
30. Rapid and accurate estimates of statistical significance for sequence database searches
31. Alignments without low-scoring regions
32. Post-processing long pairwise alignments