دورية أكاديمية
أعرض في EDS

IMSA: integrated metagenomic sequence analysis for identification of exogenous reads in a host genomic background.

التفاصيل البيبلوغرافية
العنوان: IMSA: integrated metagenomic sequence analysis for identification of exogenous reads in a host genomic background.
المؤلفون: Dimon MT; Department of Dermatology, University of California San Francisco, San Francisco, California, United States of America., Wood HM, Rabbitts PH, Arron ST
المصدر: PloS one [PLoS One] 2013 May 23; Vol. 8 (5), pp. e64546. Date of Electronic Publication: 2013 May 23 (Print Publication: 2013).
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: Electronic-Print Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
أسماء مطبوعة: Original Publication: San Francisco, CA : Public Library of Science
مواضيع طبية MeSH: Genes, Bacterial* , Genes, Viral* , Metagenome*, Microbiota/*genetics , Sequence Analysis, DNA/*methods, Algorithms ; Carcinoma, Squamous Cell/virology ; Female ; Genome, Human ; HeLa Cells ; High-Throughput Nucleotide Sequencing ; Human papillomavirus 16/genetics ; Human papillomavirus 18/genetics ; Humans ; Molecular Sequence Annotation ; Papillomavirus Infections/virology ; Sequence Alignment ; Uterine Cervical Neoplasms/virology
مستخلص: Metagenomics, the study of microbial genomes within diverse environments, is a rapidly developing field. The identification of microbial sequences within a host organism enables the study of human intestinal, respiratory, and skin microbiota, and has allowed the identification of novel viruses in diseases such as Merkel cell carcinoma. There are few publicly available tools for metagenomic high throughput sequence analysis. We present Integrated Metagenomic Sequence Analysis (IMSA), a flexible, fast, and robust computational analysis pipeline that is available for public use. IMSA takes input sequence from high throughput datasets and uses a user-defined host database to filter out host sequence. IMSA then aligns the filtered reads to a user-defined universal database to characterize exogenous reads within the host background. IMSA assigns a score to each node of the taxonomy based on read frequency, and can output this as a taxonomy report suitable for cluster analysis or as a taxonomy map (TaxMap). IMSA also outputs the specific sequence reads assigned to a taxon of interest for downstream analysis. We demonstrate the use of IMSA to detect pathogens and normal flora within sequence data from a primary human cervical cancer carrying HPV16, a primary human cutaneous squamous cell carcinoma carrying HPV 16, the CaSki cell line carrying HPV16, and the HeLa cell line carrying HPV18.
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معلومات مُعتمدة: KL2 TR000143 United States TR NCATS NIH HHS
تواريخ الأحداث: Date Created: 20130530 Date Completed: 20140107 Latest Revision: 20211021
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC3662787
DOI: 10.1371/journal.pone.0064546
PMID: 23717627
قاعدة البيانات: MEDLINE
الوصف
تدمد:1932-6203
DOI:10.1371/journal.pone.0064546