TransAlign: Using amino acids to facilitate the multiple alignment of protein-coding DNA sequences

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Bininda Emonds, Olaf R P ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; AUTOMATED ALIGNMENTS; COMPARATIVE GENOMICS; CROSS-PLATFORM; MULTIPLE ALIGNMENT; OPTIMAL ORIENTATION; PHYLOGENETIC ANALYSIS; PROTEIN-CODING GENES;

AMINO ACIDS; DNA; OPTIMAL SYSTEMS; PROTEINS;

DNA SEQUENCES;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; COMPUTER SYSTEM; CONTROLLED STUDY; DNA PROTEIN COMPLEX; DNA SEQUENCE; GENETIC CODE; OPEN READING FRAME; PHYLOGENY; PROBABILITY; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STOP CODON; ALGORITHM; BIOLOGY; CHEMISTRY; COMPUTER LANGUAGE; GENE EXPRESSION PROFILING; GENOME; GENOMICS; INFORMATION RETRIEVAL; INTERNET; NUCLEOTIDE SEQUENCE; PROCEDURES; PROTEIN SYNTHESIS; SEQUENCE ANALYSIS;

MAMMALIA;

AMINO ACID; DNA; PROTEIN;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DNA; GENE EXPRESSION PROFILING; GENOME; GENOMICS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; OPEN READING FRAMES; PHYLOGENY; PROGRAMMING LANGUAGES; PROTEIN BIOSYNTHESIS; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 25444472044     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-156     Document Type: Article

References (21)

1. Haubold B, Wiehe T: Comparative genomics: methods and applications. Naturwissenschaften 2004, 91:405-421.
2. Wernersson R, Pedersen AG: RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res 2003, 31:3537-3539.
3. Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992, 89:10915-10919.
4. Gonnet GH, Cohen MA, Benner SA: Exhaustive matching of the entire protein sequence database. Science 1992, 256:1443-1445.
5. Dayhoff MO, Schwartz RM, Orcutt BC: A model of evolutionary change in proteins. In Atlas of Protein Sequence Structure Volume 5. Edited by: Dayhoff MO. Washington, D.C.: National Biomedical Research Foundation; 1978:345-352.
6. Posada D, Crandall KA: Selecting the best-fit model of nucleotide substitution. Syst Biol 2001, 50:580-601.
7. Smith TF, Waterman MS: Identification of common molecular subsequences. J Mol Biol 1981, 147:195-197.
8. MRTRANS - CDNA alignment based on protein alignment [http://www.rfcgr.mrc.ac.uk/Registered/Option/mrtrans.html]
9. RevTrans Server [http://www.cbs.dtu.dk/services/RevTrans/]
10. Morgenstern B: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 1999, 15:211-218.
11. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S: LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 2003, 13:721-731.
12. Maddison DR, Swofford DL, Maddison WP: NEXUS: an extensible file format for systematic information. Syst Biol 1997, 46:590-621.
13. Felsenstein J: PHYLIP (Phylogeny Inference Package), version 3.6. Seattle: Department of Genome Sciences, University of Washington; 2004.
14. Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52:696-704.
15. Se-Al Homepage [http://evolve.zoo.ox.ac.uk/software.html?name=Se-Al]
16. Readseq Homepage [http://iubio.bio.indiana.edu/soft/molbio/readseq/java/]
17. HMMER: sequence analysis using profile hidden Markov models [http://hmmer.wustl.edu/]
18. NCBI Taxonomy Homepage [http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi]
19. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
20. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD: Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 2003, 31:3497-3500.
21. Wain HM, Lush M, Ducluzeau F, Povey S: Genew: the human gene nomenclature database. Nucleic Acids Res 2002, 30:169-171.