المؤلفون: Andrasi, M., Pajaziti, B., Sipos, B., Nagy, C., Hamidli, N., Gaspar, A.

المساهمون: European Regional Development Fund, National Research, Development and Innovation Office, European Commission

المصدر: Journal of Chromatography A ; volume 1626, page 461344 ; ISSN 0021-9673

مصطلحات موضوعية: Organic Chemistry, General Medicine, Biochemistry, Analytical Chemistry

الإتاحة: https://doi.org/10.1016/j.chroma.2020.461344Test
https://api.elsevier.com/content/article/PII:S0021967320306221?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S0021967320306221?httpAccept=text/plainTest

المؤلفون: Engström, Pg, Steijger, T, Sipos, B, Grant, Gr, Kahles, A, Alioto, T, Behr, J, Bertone, P, Bohnert, R, Campagna, Davide, Davis, Ca, Dobin, A, Gingeras, Tr, Goldman, N, Guigó, R, Harrow, J, Hubbard, Tj, Jean, G, Kosarev, P, Li, S, Liu, J, Mason, Ce, Molodtsov, V, Ning, Z, Ponstingl, H, Prins, Jf, Rätsch, G, Ribeca, P, Seledtsov, I, Solovyev, V, Valle, Giorgio, Vitulo, Nicola, Wang, K, Wu, Td, Zeller, G, Rgasp, Consortium

المساهمون: Laboratoire d'Informatique de Nantes Atlantique (LINA), Centre National de la Recherche Scientifique (CNRS)-Mines Nantes (Mines Nantes)-Université de Nantes (UN), The Wellcome Trust Sanger Institute [Cambridge], Centro de Regulación Genómica (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), Department of Computer Science [Royal Holloway], Royal Holloway [University of London] (RHUL), CRIBI (CRIBI), Universita degli Studi di Padova, Dipartimento di Scienze, Tecnologie e Mercati della Vite e del Vino, University of Verona (UNIVR), Sanger Institute, Wellcome Trust, Bertone, Paul [0000-0001-5059-4829], Apollo - University of Cambridge Repository

المصدر: Nature methods
Nature Methods
Nature Methods, Nature Publishing Group, 2013, epub ahead of print. ⟨10.1038/nmeth.2722⟩
Recercat. Dipósit de la Recerca de Catalunya
instname

مصطلحات موضوعية: False discovery rate, Sequence analysis, RNA Splicing, Messenger, Animals, Chromosome Mapping, Computational Biology, Exons, False Positive Reactions, High-Throughput Nucleotide Sequencing, Humans, K562 Cells, Mice, RNA, Messenger, Reproducibility of Results, Sequence Alignment, Sequence Analysis, RNA, Software, RNA-Seq, Sequence alignment, Computational biology, Biology, Biochemistry, Article, 03 medical and health sciences, Exon, 0302 clinical medicine, Empalmament (Genètica), Gens Mapatge, Molecular Biology, 030304 developmental biology, Genetics, 0303 health sciences, business.industry, Cell Biology, Gene Annotation, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 030220 oncology & carcinogenesis, RNA splicing, RNA, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, Sequence Analysis, Biotechnology

الوصف: LINA-COMBI; International audience; : High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction. We observed concordant results on real and simulated RNA-seq data, confirming the relevance of the metrics employed. Future developments in RNA-seq alignment methods would benefit from improved placement of multimapped reads, balanced utilization of existing gene annotation and a reduced false discovery rate for splice junctions.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6385fd1559cfdc01d937b50d88596646Test
http://europepmc.org/articles/PMC4018468Test

المؤلفون: Sitek, B., Sipos, B., Pfeiffer, K., Grzendowski, M., Poschmann, G., Hawranke, E., Köper, K., Klöppel, G., Meyer, H. E., Stühler, K.

المصدر: Analytical and Bioanalytical Chemistry ; volume 391, issue 1, page 361-365 ; ISSN 1618-2642 1618-2650

مصطلحات موضوعية: Biochemistry, Analytical Chemistry

الإتاحة: https://doi.org/10.1007/s00216-008-2042-8Test

المؤلفون: Behner, H., Gieres, G., Sipos, B.

المصدر: Fresenius' Journal of Analytical Chemistry ; volume 341, issue 3-4, page 301-307 ; ISSN 0937-0633 1618-2650

مصطلحات موضوعية: Biochemistry, Analytical Chemistry

الإتاحة: https://doi.org/10.1007/bf00321568Test