title: DSAP: deep-sequencing small RNA analysis pipeline.
abstract: DSAP is an automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform. The input data will go through four analysis steps in DSAP: (i) cleanup: removal of adaptors and poly-A/T/C/G/N nucleotides; (ii) clustering: grouping of cleaned sequence tags into unique sequence clusters; (iii) non-coding RNA (ncRNA) matching: sequence homology mapping against a transcribed sequence library from the ncRNA database Rfam (http://rfam.sanger.ac.uk/); and (iv) known miRNA matching: detection of known miRNAs in miRBase (http://www.mirbase.org/) based on sequence homology. The expression levels corresponding to matched ncRNAs and miRNAs are summarized in multi-color clickable bar charts linked to external databases. DSAP is also capable of displaying miRNA expression levels from different jobs using a log(2)-scaled color matrix. Furthermore, a cross-species comparative function is also provided to show the distribution of identified miRNAs in different species as deposited in miRBase. DSAP is available at http://dsap.cgu.edu.tw.
authors.affiliation: Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.
authors.forename: Po-Jung
authors.initials: PJ
authors.lastname: Huang
authors.forename: Yi-Chung
authors.initials: YC
authors.lastname: Liu
authors.forename: Chi-Ching
authors.initials: CC
authors.lastname: Lee
authors.forename: Wei-Chen
authors.initials: WC
authors.lastname: Lin
authors.forename: Richie Ruei-Chi
authors.initials: RR
authors.lastname: Gan
authors.forename: Ping-Chiang
authors.initials: PC
authors.lastname: Lyu
authors.forename: Petrus
authors.initials: P
authors.lastname: Tang
mesh_terms: D020407:Internet; D035683:MicroRNAs / Q000737:chemistry* / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D035683:MicroRNAs; D022661:RNA, Untranslated