Galaxy as a platform for identifying candidate pathogen effectors

Methods in Molecular Biology

Volumn 1127, Issue , 2014, Pages 3-15

  Cock, Peter J A ^a   Pritchard, Leighton ^a  

^a NONE

Author keywords

Bioinformatics; Classifi cation; Effectors; Galaxy; Genomics; High throughput screening; Pipeline; Sequence analysis; Workflow

Indexed keywords

MICROORGANISM PROTEIN; SIGNAL PEPTIDE; HELMINTH PROTEIN;

ARTICLE; BIOINFORMATICS; EUKARYOTE; GENE SEQUENCE; GLOBODERA PALLIDA; NEMATODE; NONHUMAN; PLANT DISEASE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN SECRETION; PROTEIN SYNTHESIS; WEB BROWSER; WORKFLOW; AMINO ACID SEQUENCE; ANIMAL; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; INTERNET; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PATHOGENICITY; PROTEIN TERTIARY STRUCTURE; SECRETION (PROCESS); SEQUENCE ANALYSIS;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; COMPUTATIONAL BIOLOGY; HELMINTH PROTEINS; INTERNET; MOLECULAR SEQUENCE DATA; NEMATODA; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84908483995     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-986-4_1     Document Type: Article

References (14)

1. Goecks J, Nekrutenko A, Taylor J, Galaxy Team (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11(8):R86
2. Blankenberg D, Kuster von G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J (2010) Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol Chapter 19:Unit 19.10.1-21
3. Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J (2010) Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinforma 11(suppl 12):S4
4. MacLean D, Kamoun S (2012) Big data in small places. Nat Biotechnol 30(1):33-34
5. Cock PJ, Grüning BA, Paszkiewicz K, Pritchard L (2013) Galaxy tools and workfl ows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 http://dx.doi.org/10.7717/peerj.167
6. Jones JT, Kumar A, Pylypenko LA, Thirugnanasambandam A, Castelli L, Chapman S, Cock PJA, Grenier E, Lilley CJ, Phillips MS, Blok VC (2009) Identifi cation and functional characterization of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematode Globodera pallida. Mol Plant Pathol 10(6):815-828
7. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340(4): 783-795
8. Krogh A, Larsson B, von Heijne G, Sonnhammer E (2001) Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J Mol Biol 305:567-580
9. Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, Mcveigh P, Takanashi T, Tsai IJ, Assefa SA, Cock PJA, Otto TD, Hunt M, Reid AJ, Sanchez-Flores A, Tsuchihara K, Yokoi T, Larsson MC, Miwa J, Maule AG, Sahashi N, Jones JT, Berriman M (2011) Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathog 7(9):e1002219
10. Whisson SC, Boevink PC, Moleleki L, Avrova AO, Morales JG, Gilroy EM, Armstrong MR, Grouffaud S, Van West P, Chapman S, Hein I, Toth IK, Pritchard L, Birch PRJ (2007) A translocation signal for delivery of oomycete effector proteins into host plant cells. Nature 450(7166):115-118
11. Win J, Morgan W, Bos J, Krasileva KV, Cano LM, Chaparro-Garcia A, Ammar R, Staskawicz BJ, Kamoun S (2007) Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. Plant Cell 19(8):2349-2369
12. Bhattacharjee S, Hiller NL, Liolios K, Win J, Kanneganti T-D, Young C, Kamoun S, Haldar K (2006) The malarial host-targeting signal is conserved in the Irish potato famine pathogen. PLoS Pathog 2(5):e50
13. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinforma 10:421
14. Moreno-Hagelsieb G, Latimer K (2008) Choosing BLAST options for better detection of orthologs as reciprocal best hits. Bioinformatics 24(3):319-324