FixPred: A resource for correction of erroneous protein sequences

Database

Volumn 2014, Issue , 2014, Pages

  Nagy, Alinda ^a   Patthy, László ^a  

^a INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMISTRY; COMPUTER PROGRAM; HUMAN; PROTEIN DATABASE;

AMINO ACID SEQUENCE; ANIMALS; DATABASES, PROTEIN; HUMANS; PROTEINS; SOFTWARE;

EID: 84906551573     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bau032     Document Type: Article

References (20)

1. Guigó, R., Flicek, P., Abril, J.F. et al. (2006) EGASP: The human ENCODE genome annotation assessment project. Genome Biol., 7 (Suppl. 1), S2.
2. Harrow, J., Nagy, A., Reymond, A. et al. (2009) Identifying protein-coding genes in genomic sequences. Genome Biol., 10, 201.
3. Nagy, A., Hegyi, H., Farkas, K. et al. (2008) Identification and correction of abnormal, incomplete and mispredicted proteins in public databases. BMC Bioinformatics, 9, 353.
4. Nagy, A. and Patthy, L. (2011) Reassessing domain architecture evolution of metazoan proteins: The contribution of different evolutionary mechanisms. Genes, 2, 578-598.
5. Nagy, A., Szláma, G., Szarka, E. et al. (2011) Reassessing domain architecture evolution of metazoan proteins: Major impact of gene prediction errors. Genes, 2, 449-501.
6. Guo, B., Zou, M. and Wagner, A. (2012) Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication. Mol. Biol. Evol., 29, 3005-3022.
7. Prosdocimi, F., Linard, B., Pontarotti, P. et al. (2012)Controversies in modern evolutionary biology: The imperative for error detection and quality control. BMC Genomics, 13, 5.
8. Zhang, X., Goodsell, J. and Norgren, R.B. Jr. (2012) Limitations of the rhesus macaque draft genome assembly and annotation. BMC Genomics, 13, 206.
9. Norgren, R.B. Jr. (2013) Improving genome assemblies and annotations for nonhuman primates. ILAR J., 54, 144-153.
10. Nagy, A. and Patthy, L. (2013) MisPred: A resource for identification of erroneous protein sequences in public databases. Database (Oxford), 2013, bat053.
11. Tress, M.L., Martelli, P.L., Frankish, A. et al. (2007) The implications of alternative splicing in the ENCODE protein complement. Proc. Natl Acad. Sci. USA, 104, 5495-5500.
12. The UniProt Consortium. (2013) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res., 41, D43-D47.
13. Flicek, P., Ahmed, I., Amode, M.R. et al. (2013) Ensembl 2013.Nucleic Acids Res., 41, D48-D55.
14. Pruitt, K.D., Tatusova, T., Brown, G.R. et al. (2013) NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy. Nucleic Acids Res., 40, D130-D135.
15. Benson, D.A., Cavanaugh, M., Clark, K. et al. (2013) GenBank. Nucleic Acids Res., 41, D36-D42.
16. Altschul, S.F., Madden, T.L., Schaffer, A.A. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
17. Rice, P., Longden, I. and Bleasby, A. (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
18. Birney, E., Clamp, M. and Durbin, R. (2004) GeneWise and Genomewise. Genome Res., 4, 988-995.
19. Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
20. Stanke, M., Steinkamp, R., Waack, S. et al. (2004) AUGUSTUS: A web server for gene finding in eukaryotes. Nucleic Acids Res., 32, W309-W312.