GASP: Gapped ancestral sequence prediction for proteins

BMC Bioinformatics

Volumn 5, Issue , 2004, Pages

  Edwards, Richard J ^a   Shields, Denis C ^a  

^a ROYAL COLLEGE OF SURGEONS IN IRELAND   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE ALGORITHMS; AMINO ACID SUBSTITUTION; BIOINFORMATICS ANALYSIS; INSERTIONS AND DELETIONS; MAXIMUM LIKELIHOOD APPROACHES; MAXIMUM LIKELIHOOD METHODS; MULTIPLE SEQUENCE ALIGNMENTS; PREDICTION ACCURACY;

ALGORITHMS; AMINO ACIDS; BIOINFORMATICS; BIOLOGY; PROTEINS; TREES (MATHEMATICS);

FORECASTING;

AMINO ACID; AVIAN PROTEIN; DNA; PROTEIN;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; DATA ANALYSIS; GENE DELETION; GENE INSERTION; HUMAN; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PREDICTION; PROBABILITY; SEQUENCE ALIGNMENT; SIMULATION; ANIMAL; BOVINAE; CHEMISTRY; CHICKEN; COMPUTER PROGRAM; COMPUTER SIMULATION; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MOUSE; PREDICTIVE VALUE; RAT;

INSERTION SEQUENCES;

AMINO ACID SEQUENCE; ANIMALS; AVIAN PROTEINS; CATTLE; CHICKENS; COMPUTER SIMULATION; DNA; EVOLUTION, MOLECULAR; HUMANS; MICE; MOLECULAR SEQUENCE DATA; PREDICTIVE VALUE OF TESTS; PROTEINS; RATS; SOFTWARE;

EID: 13244278007     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-123     Document Type: Article

References (14)

1. Zhang J, Nei M: Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods. J Mol Evol 1997, 44:S139-146.
2. Messier W, Stewart CB: Episodic adaptive evolution of primate lysozymes. Nature 1997, 385:151-154.
3. Caffrey DR, O'Neill LA, Shields DC: A method to predict residues conferring functional differences between related proteins: application to MAP kinase pathways. Protein Sci 2000, 9: 55-670.
4. Fitch WM: Toward defining course of evolution - minimum change for a specific tree topology. Systematic Zoology 1971, 20:406-416.
5. Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13: 55-556.
6. Yang Z, Kumar S, Nei M: A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 1995, 141:1641-1650.
7. Pupko T, Pe'er I, Shamir R, Graur D: A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol Biol Evol 2000, 17:890-896.
8. Koshi JM, Goldstein RA: Probabilistic reconstruction of ancestral protein sequences. J Mol Evol 1996, 42:313-320.
9. Phylogenetic Analysis by Maximum Likelihood (PAML) [http://abacus.gene.ucl.ac.uk/software/paml.html]
10. The Newick tree format [http://evolution.genetics.washington.edu/phylip/newicktree.html]
11. Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992, 8:275-282.
12. TreeExplorer manual [http://evolgen.biol.metro-u.ac.jp/TE/TE_man.html]
13. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003, 31:365-370.
14. BioEdit Sequence Alignment Editor for Windows 95/98/NT [http://www.mbio.ncsu.edu/BioEdit/bioedit.html]