Compressive genomics for protein databases

Bioinformatics

Volumn 29, Issue 13, 2013, Pages

  Daniels, Noah M ^a   Gallant, Andrew ^a   Peng, Jian ^b,c   Cowen, Lenore J ^a   Baym, Michael ^b,c,d   Berger, Bonnie ^b,c  

^a Tufts University   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; GENOMICS; INFORMATION PROCESSING; PROCEDURES; PROTEIN DATABASE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; ARTICLE; METHODOLOGY;

ALGORITHMS; DATA COMPRESSION; DATABASES, PROTEIN; GENOMICS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84879920277     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt214     Document Type: Conference Paper

References (31)

1. Altschul, S.F. et al. (1997) Lipman. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Boratyn, G.M. et al. (2012) Domain enhanced lookup time accelerated BLAST. Biol. Direct., 7, 12.
3. Brandon, M.C. et al. (2009) Data structures and compression algorithms for genomic sequence data. Bioinformatics, 25, 1731-1738.
4. Cameron, M. et al. (2007) Clustered sequence representation for fast homology search. J. Comput. Biol., 14, 594-614.
5. Chen, F. et al. (2007) Assessing performance of orthology detection strategies applied to eukaryotic genomes. PloS One, 2, e383.
6. Chen, X. et al. (2002) DNACompress: Fast and effective DNA sequence compression. Bioinformatics, 18, 1696-1698.
7. Cherry, J.M. et al. (2012) Wong. Saccharomyces Genome Database: The genomics resource of budding yeast. Nucleic Acids Res., 40, D700-D705.
8. Daniels, N.M. et al. (2012) Cowen. SMURFLite: Combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone. Bioinformatics, 28, 1216-1222.
9. Griesemer, R. et al. (2009) The GO Programming Language. http://golang.org/(3 June 2013, date last accessed).
10. Gross, M. (2011) Riding the wave of biological data. Curr. Biol., 21, R204-R206.
11. Hachiya, T. et al. (2009) Accurate identification of orthologous segments among multiple genomes. Bioinformatics, 25, 853-860.
12. Huttenhower, C. and Hofmann, O. (2010) A quick guide to large-scale genomic data mining. PLoS Comput. Biol., 6, e1000779.
13. Kahn, S.D. (2011) On the future of genomic data. Science, 331, 728-729.
14. Kircher, M and Kelso, J. (2010) High-throughput DNA sequencing-concepts and limitations. BioEssays, 32, 524-536.
15. Kortschak, R.D (2011) BioGo. http://github.org/kortschak/biogo (3 June 2013, date last accessed).
16. Kosloff, M. and Kolodny, R. (2008) Sequence-similar, structure-dissimilar protein pairs in the PDB. Proteins, 71, 891-902.
17. Kumar, A. and Cowen, L. (2009) Augmented training of hidden Markov models to recognize remote homologs via simulated evolution. Bioinformatics, 25, 1602-1608.
18. Kumar, A. and Cowen, L. (2010) Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution. Bioinformatics, 26, i287-i293.
19. Loewenstein, Y. et al. (2009) Protein function annotation by homology-based inference. Genome Biol., 10, 207.
20. Loh, P.R. et al. (2012) Compressive genomics. Nat. Biotechnol., 30, 627-630.
21. McDonnell, A. et al. (2006) Fold recognition and accurate sequence-structure alignment of sequences directing -sheet proteins. Proteins, 63, 976-985.
22. Moreno-Hagelsieb, G. and Latimer, K. (2008) Choosing BLAST options for better detection of orthologs as reciprocal best hits. Bioinformatics, 24, 319-324.
23. Moult, J. et al. (2011) Critical assessment of methods of protein structure prediction (CASP) - round IX. Proteins, 79 (Suppl. 10), 74-90.
24. Murzin, A. et al. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
25. Needleman, S.B. and Wunsch, C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
26. Remmert, M. et al. (2012) HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods, 9, 173-175.
27. Rost, B. et al. (2004) The PredictProtein server. Nucleic Acids Res., 32, W321-W326.
28. Schatz, M.C. et al. (2010) Cloud computing and the DNA data race. Nat. Biotechnol., 28, 691-693.
29. Singh, R. et al. (2008) Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc. Natl. Acad. Sci. USA, 105, 12763-12768.
30. Söding, J. et al. (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res., 33, W244-W248.
31. Tatusov, R.L. et al. (2000) The COG database: A tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Research, 28, 33-36.