SANSparallel: Interactive homology search against Uniprot

Nucleic Acids Research

Volumn 43, Issue W1, 2015, Pages W24-W29

  Somervuo, Panu ^a,b   Holm, Liisa ^a,b  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CLIENT SERVER APPLICATION; COMPUTER AIDED DESIGN; COMPUTER ANALYSIS; COMPUTER INTERFACE; DATA BASE; INFORMATION PROCESSING; PRIORITY JOURNAL; SANSPARALLEL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SOFTWARE; WEB BROWSER; COMPUTER PROGRAM; INTERNET; PROCEDURES; PROTEIN DATABASE; SEQUENCE ANALYSIS;

ALGORITHMS; DATABASES, PROTEIN; INTERNET; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 84979856621     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv317     Document Type: Article

References (27)

1. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. McGinnis, S. and Madden, T.L. (2004) BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res., 32, W20-W25.
3. Analysis Tool Web Services from the EMBL-EBI. (2013) Nucleic Acids Res., 41, W597-W600.
4. Finn, R.D., Clements, J. and Eddy, S.R. (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res., 39, W29-W37.
5. Sun, S., Chen, J., Li, W., Altinatas, I., Lin, A., Peltier, S., Stocks, K., Allen, E.E., Ellisman, M., Grethe, J. et al. (2011) Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res., 39, D546-D551.
6. Heger, A., Korpelainen, E., Hupponen, T., Mattila, K., Ollikainen, V. and Holm, L. (2008) Pairs DB atlas of protein sequence space. Nucleic Acids Res., 36, D276-D280.
7. Rattei, T., Arnold, R., Tischler, P., Lindner, D., Stümpflen, V. and Mewes, H.W. (2006) SIMAP: the similarity matrix of proteins. Nucleic Acids Res., 34, D252-D256.
8. The Uni Prot Consortium. (2015) Uni Prot: a hub for protein information. Nucleic Acids Res., 43, D204-D212.
9. Koskinen, P. and Holm, L. (2012) SANS: high-throughput retrieval of protein sequences allowing 50% mismatches. Bioinformatics, 28, i438-i443.
10. Kent, W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
11. Zhao, Y., Tang, H. and Ye, Y. (2012) RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics, 28, 125-126.
12. Hauswedell, H., Singer, J. and Reinert, K. (2014) Lambda: the local aligner for massive biological data. Bioinformatics, 30, i349-i355.
13. Kielbasa, S.M., Wan, R., Sato, K., Horton, P. and Frith, M.C. (2011) Adaptive seeds tame genomic sequence comparison. Genome Res., 21, 487-493.
14. Edgar, Robert C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
15. Buchfink, B., Xie, C. and Huson, D.H. (2014) Fast and sensitive protein alignment using DIAMOND. Nat. Methods, 12, 59-60.
16. Roytberg, M., Gambin, A., Noé, L., Lasota, S., Furletova, E., Szczurek, E. and Kucherov, G. (2009) On subset seeds for protein alignment. IEEE/ACM Trans. Comput. Biol. Bioinform., 6, 483-494.
17. Pearson, W.R. (1996) Effective protein sequence comparison. Methods Enzymol., 266, 227-258.
18. Brown, N.P., Leroy, C. and Sander, C. (1998) MView: a web-compatible database search or multiple alignment viewer. Bioinformatics., 14, 380-381.
19. Wheeler, T.J., Clements, J. and Finn, R.D. (2014) Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. BMC Bioinformatics., 15, 7.
20. Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M. and Barton, G.J. (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics., 25, 1189-1191.
21. Korf, I., Yandell, M. and Bedell, J. (2003) Blast. O'Reilly & Associates, Sebastopol, CA, ISBN-13: 978-0596002992.
22. Holm, L. and Rosenström, P. (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res., 38, W545-W549.
23. Garlant, L., Koskinen, P., Liu, Y., Nykyri, J., Ahamed, S., Rouhiainen, L., Laine, P., Paulin, L., Auvinen, P., Holm, L. et al. (2013) Genome sequence of Dickeya solani, a new soft rot pathogen of potato, suggests its emergence may be related to a novel combination of non-ribosomal peptide/polyketide synthetase clusters. Diversity, 5, 824-842.
24. Ahola, V., Lehtonen, R., Somervuo, P., Salmela, L., Koskinen, P., Rastas, P., Välimäki, N., Paulin, L., Kvist, J., Wahlberg, N. et al. (2014) The Glanville fritillary butterfly retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera. Nat. Commun., 5, 4737.
25. Koskinen, P., Toronen, P., Nokso-Koivisto, J. and Holm, L. (2014) PANNZER-high-throughput functional annotation of uncharacterized proteins in an error-prone environment. Bioinformatics, doi:10.1093/bioinformatics/btu851.
26. O'Donoghue, S.I., Sabir, K.S., Kalemanov, M., Stolte, C., Wellmann, B., Ho, V., Roos, M., Perdigão, N., Buske, F.A., Heinrich, J. et al. (2015) Aquaria: simplifying discovery and insight from protein structures. Nat. Methods, 12, 98-99.
27. Rost, B. and Sander, C. (1994) Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 19, 55-72.