Amino acid substitution matrices from an information theoretic perspective

Journal of Molecular Biology

Volumn 219, Issue 3, 1991, Pages 555-565

  Altschul, Stephen F ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

alignment algorithms; homology; pattern recognition; sequence comparison; statistical significance

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; PATTERN RECOGNITION; PRIORITY JOURNAL;

ALGORITHMS; AMINO ACID SEQUENCE; COMPARATIVE STUDY; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEINS; SEQUENCE HOMOLOGY, NUCLEIC ACID; THERMODYNAMICS;

EID: 0025878149     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/0022-2836(91)90193-A     Document Type: Article

References (60)

1. A nonlinear measure of subalignment similarity and its significance levels
2. Protein database searches for multiple alignments
3. Basic local alignment search tool
4. A sensitive procedure to compare amino acid sequences
5. Sequence and topology of a model intracellular membrane protein. El glycoprotein. from a coronavirus
6. The Erdos-Renyl strong law for pattern matching with a given proportion of mismatches
7. An extreme value theory for sequence matching
8. Stochastic scrabble large deviations Cor sequences with scores
9. Molecular sequence databases and their uses
10. Molecular cloning of the cDNA for two major androgen-dependent secretory proteins of 18.5 kilodaltons synthesized by the rat epididymis
11. The significance of protein sequence similarities
12. fhuC and fhuD genes for iron(III)-ferrichrome transport into Escherichia coli K-12
13. Crystallographic refinement of human serum retinol binding protein at 2 Å resolution
14. Comparison of sequences from the malB regions of Salmonella lyphimurium and Enterobacter aerogenes with Escherichia coli K12: a potential new regulatory site in the interoperonie region
15. A model of evolutionary change in proteins
16. Strong limit laws of empirical functionals for large exceedences of partial sums of I.I.D. variables
17. 2μ-globulin super-family
18. Aligning amino acid sequences: comparison of commonly used methods
19. Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries
20. Profile analysis: detection of distantly related proteins
21. Nucleotide binding by membrane components of bacterial periplasmic binding protein-dependent transport systems
22. A family of related ATP-binding subunits coupled to many distinct biological processes in bacteria
23. The spatial distribution of fixed mutations within genes coding for proteins
24. Sequences of Escherichia coli uvrA gene and protein reveal two potential ATP binding sites
25. Amino acid sequence of human plasma α IB-glycoprotein: homology to the immunoglobulin supergene family
26. The nucleotide sequence of the lux E gene of Vibrio harveyi and a comparison of the amino acid sequences of the acyl-protein synthetases from V. harveyi and V. fischeri
27. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
28. Statistical composition of high-scoring segments from molecular sequences
29. The mRNA for a proteinase inhibitor related to the HI-30 domain of inter-α-trypsin inhibitor also encodes α-1-microglobulin (protein HC)
30. Rapid and sensitive protein similarity searches
31. 551
32. A general method applicable to the search for similarities in the amino acid sequences of two proteins
33. Nucleotide sequence of the genome of eggplant mosaic tymovirus
34. DNA sequence of the metC gene and its flanking regions from Salmonella typhimurium LT2 and homology with the corresponding sequence of Escherichia coli
35. Detecting homology of distantly related proteins with consensus sequences
36. Improved tools for biological sequence comparison
37. Immunoglobulin genes of different subgroups are interdigitated within the VK locus
38. Is apolipoprotein D a mammalian bilin-binding protein?
39. Primary structure of c-kit: relationship with the CSF-I/PDGF receptor kinase family-oncogenic activation of v-kit involves deletion of extracellular domain and C terminus
40. Molecular cloning and sequence analysis of 3-hydroxy-3-methylglutaryl-coenzyme A reduetase from the human parasite Schistosoma masoni
41. New scoring matrix for amino acid residue exchanges based on residue characteristic physical parameters
42. The amino acid sequence of leghaemoglobin I from root nodules of broad bean (Vicia faba L.)
43. Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA
44. Amino acid substitutions in structurally related proteins. A pattern recognition approach. Determination of a new and efficient scoring matrix
45. Matrices for detecting distant relationships
46. On the theory and computation of evolutionary distances
47. Pattern recognition in genetic sequences by mismatch density
48. The Fey receptor of natural killer cells is a phospholipid-linked membrane protein
49. Identification of common molecular subsequences
50. The statistical distribution of nucleic acid similarities
51. Identifying protein-binding sites from unaligned DNA fragments
52. Amino acid sequence of a major globin from the sea cucumber Paracaudina chilensis
53. Identification of protein sequence homology by consensus template alignment
54. Primary structure of rat brain prostaglandin D synthetase deduced from cDNA sequence
55. Fitting discrete probability distributions to evolutionary events
56. 1 B-glycoprotein in human
57. Phase transitions in sequence matches and nucleic acid structure
58. On the PAM matrix model of protein evolution
59. Nucleotide sequence of the hygromycin B phosphotransferase gene from Streptomyces hygroscopius