A novel hybrid gene prediction method employing protein multiple sequence alignments

Bioinformatics

Volumn 27, Issue 6, 2011, Pages 757-763

  Keller, Oliver ^a   Kollmar, Martin ^b   Stanke, Mario ^c   Waack, Stephan ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

^b MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^c UNIVERSITY OF GREIFSWALD   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA;

DYNEIN ADENOSINE TRIPHOSPHATASE;

ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; EXON; GENETICS; HUMAN; INFORMATION PROCESSING; METHODOLOGY; MULTIGENE FAMILY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; AUTOMATIC DATA PROCESSING; COMPUTATIONAL BIOLOGY; DYNEINS; EXONS; HUMANS; MODELS, GENETIC; MULTIGENE FAMILY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 79952614033     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr010     Document Type: Article

References (23)

1. Attwood,T.K. and Beck,M.E. (1994) Prints-a protein motif fingerprint database. Protein Eng., 7, 841-848.
2. Attwood,T.K. et al. (2003) Prints and its automatic supplement, preprints. Nucleic Acids Res., 31, 400-402.
3. Birney,E. et al. (2004) Genewise and genomewise. Genome Res., 14, 988-995.
4. Castellana,N.E et al. (2008) Discovery and revision of arabidopsis genes by proteogenomics. Proc. Natl Acad. Sci. USA, 105, 21034-21038.
5. Cui,X. et al. (2007) Homology search for genes. Bioinformatics, 23, i97-i103.
6. Harrow,J. et al. (2009) Identifying protein-coding genes in genomic sequences. Genome Biol., 10, 201.
7. Henikoff,S. and Henikoff,J.G. (1991) Automated assembly of protein blocks for database searching. Nucleic Acids Res., 19, 6565-6572.
8. Henikoff,S. et al. (1990) Finding protein similarities with nucleotide sequence databases. Methods Enzymol., 183, 111-132.
9. Henikoff,S. et al. (1999) Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations. Bioinformatics, 15, 471-479.
10. Hunter,S. et al. (2009) Interpro: the integrative protein signature database. Nucleic Acids Res., 37, D211-D215.
11. Keller,O. et al. (2008) Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species. BMC Bioinformatics, 9, 278.
12. Kent,W.J. (2002) Blat-the blast-like alignment tool. Genome Res., 12, 656-664.
13. Metzker,M.L. (2010) Sequencing technologies - the next generation. Nat. Rev. Genet., 11, 31-46.
14. Meyer,I.M. and Durbin,R. (2004) Gene structure conservation aids similarity based gene prediction. Nucleic Acids Res., 32, 776-783.
15. Odronitz,F. and Kollmar,M. (2006) Pfarao: a web application for protein family analysis customized for cytoskeletal and motor proteins (cymobase). BMC Genomics, 7, 300.
16. Odronitz,F. et al. (2008) Webscipio: An online tool for the determination of gene structures using protein sequences. BMC Genomics, 9, 422.
17. Pietrokovski,S. et al. (1996) The blocks database-a system for protein classification. Nucleic Acids Res., 24, 197-200.
18. Quevillon,E. et al. (2005) Interproscan: protein domains identifier. Nucleic Acids Res., 33, W116-W120.
19. Slater,G.S.C. and Birney,E. (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics, 6, 31.
20. Stanke,M. and Waack,S. (2003) Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics, 19 (Suppl. 2), 215-215.
21. Stanke,M. et al. (2006a) Augustus at egasp: using est, protein and genomic alignments for improved gene prediction in the human genome. Genome Biol., 7 (Suppl. 1), 1-8.
22. Stanke,M. et al. (2006b) Gene prediction in eukaryotes with a generalized hidden markov model that uses hints from external sources. BMC Bioinformatics, 7, 62-62.
23. Stanke,M. et al. (2008) Using native and syntenically mapped cdna alignments to improve de novo gene finding. Bioinformatics, 24, 637-644.