Java GUI for InterProScan (JIPS): A tool to help process multiple InterProScans and perform ortholog analysis

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Syed, Aijazuddin ^a   Upton, Chris ^a  

^a UNIVERSITY OF VICTORIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL FUNCTIONS; COMPARATIVE STUDIES; LOCAL DATABASE; OPTIMAL RESULTS; POST-GENOMIC ANALYSIS; PROTEIN SEQUENCES; PROTEIN SIGNATURES; STRUCTURAL MOTIFS;

COMPUTER SOFTWARE; GENES; GRAPHICAL USER INTERFACES; JAVA PROGRAMMING LANGUAGE; TOOLS;

DATABASE SYSTEMS;

AMINO ACID SEQUENCE; ARTICLE; COMPARATIVE STUDY; EQUIPMENT DESIGN; GENETIC ANALYSIS; GENETIC DATABASE; INFORMATION PROCESSING; INFORMATION PROCESSING DEVICE; INTERPRO; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PROTEIN ANALYSIS; PROTEIN FUNCTION; SAMPLE SIZE; SEARCH ENGINE; VIRUS GENOME; ALGORITHM; CHEMISTRY; COMPUTER INTERFACE; COMPUTER LANGUAGE; COMPUTER PROGRAM; MOLECULAR GENETICS; PROCEDURES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

PROTEIN;

ALGORITHMS; AMINO ACID SEQUENCE; MOLECULAR SEQUENCE DATA; PROGRAMMING LANGUAGES; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 33750430643     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-462     Document Type: Article

References (20)

1. Liolios K, Tavernarakis N, Hugenholts P, Kyrpides NC: The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res 2006, 34:D332-D334.
2. Genome Sequencing Projects [http://www.genomesonline.org]
3. GenBank statistics [http://www.ncbi.nlm.nib.gov/Genbank/ genbankstats.html]
4. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
5. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R: InterProSacn: protein domains identifier. Nucleic Acids Res 2005, 33:W116-W120.
6. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, Gouzy J, Griffith-Jones S, Haft D, Hermjakob H, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Orchard S, Pagni M, Peyruc D, Ponting CP, Servant F, Sigrist CJ, InterPro Consortium: InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform 2002, 3:225-235.
7. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Masle J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH: InterPro, progress and status in 2005. Nucleic Acids Res 2005, 33:D201-D205.
8. Tutorial for InterPro [http://www.embl-ebi.ac.uk/interpro/tutorial.html]
9. Whitney J, Esteban DJ, Upton C: Recent Hits Acquired by BLAST (ReHAB): a tool to identify new hits in sequence similarity searches. BMC Bioinformatics 2005, 6:23.
10. Pearson WR: Flexible sequence similarity searching with the FASTA3 program package. Method Mol Biol 2000, 132:185-219.
11. Hulo N, Bairoch A, Bulliard V, Cerutti L, De Castro E, Langendijk-Genevaux PS, Pagni M, Sigrist CJ: The PROSITE database. Nucleic Acids Res 2006, 34:D227-D230.
12. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR: The Pfam protein families database. Nucleic Acids Res 2004, 32:D138-D141.
13. Web-based InterProScan at EBI [http://www.ebi.ac.uk/InterProScan]
14. The Viral Bioinformatics Resource Center [http://www.vbrc.org]
15. Ehlers A, Osborne J, Slack S, Rober RL, Upton C: Poxvirus Orthologous Clusters (POCs) Bioinformatics 2002, 18:1544-1545.
16. Brodie R, Smith AJ, Roper R. Tcherepanov V, Upton C: Base-By-Base: single nucleotide-level analysis of whole viral genome alignments. BMC Bioinformatics 2004, 5:96.
17. Client/Server Architecture [http://www.sei.cmu.edu/str/descriptions/ clientserver_body.html]
18. Installing JIPS [http://www.virology,ca/techDoc/softwaredevelopment/jips/ install]
19. Edgar RC: MUSCLE: multiple sequence aligment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797.
20. Viral Bioinformatics-Canada [http://www.virology.ca]