{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T05:20:11Z","timestamp":1674710411197},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We present a plug-in for Pathway Tools, an integrated systems biology software to create, maintain and query Pathway\/Genome Databases. Fully integrated into the graphical user interface and menu, this plug-in extends the application's functionality by the ability to create multiple sequence alignments, systematically annotate insertion sequence (IS) elements and analyse their activity by cross-species comparison tools. Microarray probes can be automatically mapped to target genes, and expression data obtained with these arrays can be transformed into input formats needed to visualize them in the various omics viewers of Pathway Tools. The plug-in API itself allows developers to integrate their own functions into the Pathway Tools menu.<\/jats:p>\n               <jats:p>Availability: Binaries are freely available for non-commercial users at http:\/\/genome.tugraz.at\/PGDBToolbox\/ and can be used on all platforms supported by Pathway Tools. A user guide is freely available at: http:\/\/genome.tugraz.at\/PGDBToolbox\/documentation.shtml.<\/jats:p>\n               <jats:p>Contact: \u00a0ptools@acib.at<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts431","type":"journal-article","created":{"date-parts":[[2012,7,7]],"date-time":"2012-07-07T02:06:56Z","timestamp":1341626816000},"page":"2283-2284","source":"Crossref","is-referenced-by-count":0,"title":["A sequence comparison and gene expression data integration add-on for the Pathway Tools software"],"prefix":"10.1093","volume":"28","author":[{"given":"Peter M.","family":"Krempl","sequence":"first","affiliation":[{"name":"1,2 \u00a01ACIB, Petersgasse 14, 8010 Graz, 2Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz and 3Institute of Applied Microbiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juergen","family":"Mairhofer","sequence":"additional","affiliation":[{"name":"1,2 \u00a01ACIB, Petersgasse 14, 8010 Graz, 2Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz and 3Institute of Applied Microbiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gerald","family":"Striedner","sequence":"additional","affiliation":[{"name":"1,2 \u00a01ACIB, Petersgasse 14, 8010 Graz, 2Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz and 3Institute of Applied Microbiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gerhard G.","family":"Thallinger","sequence":"additional","affiliation":[{"name":"1,2 \u00a01ACIB, Petersgasse 14, 8010 Graz, 2Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz and 3Institute of Applied Microbiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,7,5]]},"reference":[{"key":"2023012512561008100_bts431-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012512561008100_bts431-B2","doi-asserted-by":"crossref","first-page":"D473","DOI":"10.1093\/nar\/gkp875","article-title":"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway\/genome databases","volume":"38","author":"Caspi","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012512561008100_bts431-B3","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1007\/s00239-011-9439-2","article-title":"Insertion sequence-driven evolution of Escherichia coli in chemostats","volume":"72","author":"Gaff\u00e9","year":"2011","journal-title":"J. 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