{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T10:40:09Z","timestamp":1761561609301},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: FX is an RNA-Seq analysis tool, which runs in parallel on cloud computing infrastructure, for the estimation of gene expression levels and genomic variant calling. In the mapping of short RNA-Seq reads, FX uses a transcriptome-based reference primarily, generated from ~160 000 mRNA sequences from RefSeq, UCSC and Ensembl databases. This approach reduces the misalignment of reads originating from splicing junctions. Unmapped reads not aligned on known transcripts are then mapped on the human genome reference. FX allows analysis of RNA-Seq data on cloud computing infrastructures, supporting access through a user-friendly web interface.<\/jats:p>\n               <jats:p>Availability: FX is freely available on the web at (http:\/\/fx.gmi.ac.kr), and can be installed on local Hadoop clusters. Guidance for the installation and operation of FX can be found under the \u2018Documentation\u2019 menu on the website.<\/jats:p>\n               <jats:p>Contact: \u00a0jeongsun@snu.ac.kr; jongil@snu.ac.kr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts023","type":"journal-article","created":{"date-parts":[[2012,1,19]],"date-time":"2012-01-19T01:59:28Z","timestamp":1326938368000},"page":"721-723","source":"Crossref","is-referenced-by-count":56,"title":["FX: an RNA-Seq analysis tool on the cloud"],"prefix":"10.1093","volume":"28","author":[{"given":"Dongwan","family":"Hong","sequence":"first","affiliation":[{"name":"1 Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, 2Cancer Genomics Branch and Research Institute and Hospital, National Cancer Center, Goyang-si 410-769, 3Department of Computer Science and Engineering, Ewha Womans University, Seoul 120-750, 4Department of Biochemistry, Seoul National University College of Medicine, 5Department of Biomedical Sciences, Seoul National University Graduate School, 6Psoma Therapeutics Inc., Seoul 110\u2212799, 7Macrogen Inc., Seoul 153-023 and 8Axeq Technologies, Rockville, MD 20850, USA"},{"name":"1 Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, 2Cancer Genomics Branch and Research Institute and Hospital, National Cancer Center, Goyang-si 410-769, 3Department of Computer Science and Engineering, Ewha Womans University, Seoul 120-750, 4Department of Biochemistry, Seoul National University College of Medicine, 5Department of Biomedical Sciences, Seoul National University Graduate School, 6Psoma Therapeutics Inc., Seoul 110\u2212799, 7Macrogen Inc., Seoul 153-023 and 8Axeq Technologies, Rockville, MD 20850, USA"}]},{"given":"Arang","family":"Rhie","sequence":"additional","affiliation":[{"name":"1 Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, 2Cancer Genomics Branch and Research Institute and Hospital, National Cancer Center, Goyang-si 410-769, 3Department of Computer Science and Engineering, Ewha Womans University, Seoul 120-750, 4Department of Biochemistry, Seoul National University College of Medicine, 5Department of Biomedical Sciences, Seoul National University Graduate School, 6Psoma Therapeutics Inc., Seoul 110\u2212799, 7Macrogen Inc., Seoul 153-023 and 8Axeq Technologies, Rockville, MD 20850, USA"},{"name":"1 Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, 2Cancer Genomics Branch and Research Institute and Hospital, National Cancer Center, Goyang-si 410-769, 3Department of Computer Science and Engineering, Ewha Womans University, Seoul 120-750, 4Department of Biochemistry, Seoul National University College of Medicine, 5Department of Biomedical Sciences, Seoul National University Graduate School, 6Psoma Therapeutics Inc., Seoul 110\u2212799, 7Macrogen Inc., Seoul 153-023 and 8Axeq Technologies, Rockville, MD 20850, USA"},{"name":"1 Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, 2Cancer Genomics Branch and Research Institute and Hospital, National Cancer Center, Goyang-si 410-769, 3Department of Computer Science and Engineering, Ewha Womans University, Seoul 120-750, 4Department of Biochemistry, Seoul National University College of Medicine, 5Department of Biomedical Sciences, Seoul National University Graduate School, 6Psoma Therapeutics Inc., Seoul 110\u2212799, 7Macrogen Inc., Seoul 153-023 and 8Axeq Technologies, Rockville, MD 20850, USA"},{"name":"1 Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, 2Cancer Genomics Branch and Research Institute and Hospital, National Cancer Center, Goyang-si 410-769, 3Department of Computer Science and Engineering, Ewha Womans University, Seoul 120-750, 4Department of Biochemistry, Seoul National University College of Medicine, 5Department of Biomedical Sciences, Seoul National University Graduate School, 6Psoma Therapeutics Inc., Seoul 110\u2212799, 7Macrogen Inc., Seoul 153-023 and 8Axeq Technologies, Rockville, MD 20850, USA"}]},{"given":"Sung-Soo","family":"Park","sequence":"additional","affiliation":[{"name":"1 Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, 2Cancer Genomics Branch and Research Institute and Hospital, National Cancer Center, Goyang-si 410-769, 3Department of Computer Science and Engineering, Ewha Womans University, Seoul 120-750, 4Department of Biochemistry, Seoul National University College of Medicine, 5Department of Biomedical Sciences, Seoul National University Graduate School, 6Psoma Therapeutics Inc., Seoul 110\u2212799, 7Macrogen Inc., Seoul 153-023 and 8Axeq Technologies, Rockville, MD 20850, USA"}]},{"given":"Jongkeun","family":"Lee","sequence":"additional","affiliation":[{"name":"1 Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, 2Cancer Genomics Branch and Research Institute and Hospital, National Cancer Center, Goyang-si 410-769, 3Department of Computer Science and Engineering, Ewha Womans University, Seoul 120-750, 4Department of Biochemistry, Seoul National University College of Medicine, 5Department of Biomedical Sciences, Seoul National University Graduate School, 6Psoma Therapeutics Inc., Seoul 110\u2212799, 7Macrogen Inc., Seoul 153-023 and 8Axeq Technologies, Rockville, MD 20850, USA"}]},{"given":"Young Seok","family":"Ju","sequence":"additional","affiliation":[{"name":"1 Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, 2Cancer Genomics Branch and Research Institute and Hospital, National Cancer Center, Goyang-si 410-769, 3Department of Computer Science and Engineering, Ewha Womans University, Seoul 120-750, 4Department of Biochemistry, Seoul National University College of Medicine, 5Department of Biomedical Sciences, Seoul National University Graduate School, 6Psoma Therapeutics Inc., Seoul 110\u2212799, 7Macrogen Inc., Seoul 153-023 and 8Axeq Technologies, Rockville, MD 20850, USA"},{"name":"1 Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, 2Cancer Genomics Branch and Research Institute and Hospital, National Cancer Center, Goyang-si 410-769, 3Department of Computer Science and Engineering, Ewha Womans University, Seoul 120-750, 4Department of Biochemistry, Seoul National University College of Medicine, 5Department of Biomedical Sciences, Seoul National University Graduate School, 6Psoma Therapeutics Inc., Seoul 110\u2212799, 7Macrogen Inc., Seoul 153-023 and 8Axeq Technologies, Rockville, MD 20850, USA"}]},{"given":"Sujung","family":"Kim","sequence":"additional","affiliation":[{"name":"1 Genomic 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