Indexing and retrieval for genomic databases

IEEE Transactions on Knowledge and Data Engineering

Volumn 14, Issue 1, 2002, Pages 63-78

  Williams, Hugh E ^a,b   Zobel, Justin ^a,b  

^a IEEE   (Australia)

^b RMIT UNIVERSITY   (Australia)

Author keywords

Genomic and scientific databases; Homology search; Indexing; Local alignment

Indexed keywords

GENOMIC DATABASES; HOMOLOGY SEARCH; LOCAL ALIGNMENT;

ALGORITHMS; AMINO ACIDS; DATA STRUCTURES; DATABASE SYSTEMS; DNA SEQUENCES; INDEXING (OF INFORMATION); MOLECULAR BIOLOGY;

INFORMATION RETRIEVAL SYSTEMS;

EID: 0036184046     PISSN: 10414347     EISSN: None     Source Type: Journal    
DOI: 10.1109/69.979973     Document Type: Article

References (58)

1. Issues in searching molecular sequence databases
2. Basic local alignment search tool
3. Amino acid substitution matrices from an information theoretic perspective
4. A protein alignment scoring system sensitive at all evolutionary distances
5. Local alignment statistics
6. Gapped blast and PSI-blast: A new generation of protein database search programs
7. Searching DNA databases for similarities to DNA sequences: When is a match significant?
8. The SWISS-PROT protein sequence data bank and its new supplement TREMBL
9. Superfamily classification in PIR-international protein sequence database
10. Protein sequence alignment and database scanning
11. GenBank
12. Flash: A fast look-up algorithm for string homology
13. Aligning two sequences within a specified diagonal band
14. A new five-year plan for the US human genome project
15. New goals for the US human genome project: 1998-2003
16. Universal codeword sets and representations of the integers
17. A rapid access motif database (RAMdb) with a search algorithm for the retrieval patterns in nucleic acids or protein databanks
18. The PIR-international protein sequence database
19. Run-length encodings
20. Methods for assessing the statistical significance of molecular sequence features by using general scoring scheme
21. Sequence and transcriptional regulation of com101a, a locus required for genetic transformation in haemophilus influenzae
22. Rapid and sensitive protein similarity searches
23. Self-indexing inverted files for fast text retrieval
24. Advances in sequence assembly
25. Searching the protein database
26. Rapid and sensitive sequence comparison with FASTP and FASTA
27. Comparison of methods for searching protein-sequence databases
28. Protein sequence comparison and protein evolution
29. Improved tools for biological sequence comparison
30. Dynamic programming algorithms for biological sequence comparison
31. WORDUP: An efficient algorithm for discovering statistically significant patterns in DNA sequences
32. The EMBL data library
33. Detection of significant patterns by compression algorithms: The case of approximate tandem repeats in DNA sequences
34. Sensitivity and selectivity in protein similarity searches: A comparison of Smith-Waterman in hardware to BLAST and FASTA
35. Identification of common molecular subsequences
36. Improved sensitivity in nucleic acid database searches using application-specific scoring matrices
37. Chemical synthesis of a gene for human epidermal growth factor urogastrone and its expression in yeast
38. Rapid similarity searches of nucleic acid and protein data banks
39. Compressed indexing for genomic retrieval
40. Indexing and retrieval for genomic databases
41. Effective query filtering for fast homology searching
42. Indexing nucleotide databases for fast query evaluation
43. Compression of nucleotide databases for fast searching
44. Compressing integers for fast file access
45. The portable dictionary of the mouse genome: A personal database for gene mapping and molecular biology
46. Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm
47. Statistics of local complexity in amino acid sequences and sequence databases
48. Finding approximate matches in large lexicons
49. Searching large lexicons for partially specified terms using compressed inverted files