An update on sORFs.org: a repository of small ORFs identified by ribosome profiling.
An update on sORFs.org: a repository of small ORFs identified by ribosome profiling.
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DOI：
10.1093/nar/gkx1130
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Menschaert G
中科院分区：
文献类型：
--
作者：
Olexiouk V;Van Criekinge W;Menschaert G
sORFs.org：www.sorfs.org）是通过核糖体分析（RIBO-seq）鉴定的小开放阅读框架（sORF）的公共储存库。此更新详细说明了自首次发布以来实施的主要改进。sORFs.org现在还支持另外三个物种（斑马鱼，大鼠和秀丽隐杆线虫），目前包括78个RIBO-seq数据集，与最初版本中处理的三个数据集相比，有了巨大的增加。因此，构建了一种新的流水线，其也使得能够在仅包含延长的RIBO-seq数据的RIBO-seq数据集中进行sORF检测，而先前，匹配起始RIBO-seq数据对于描绘sORF是必要的。此外，设计了一种新的噪声过滤算法，能够将具有真实核糖体活性的sORF从模拟噪声中区分出来，从而降低了假阳性识别率。其他物种的纳入也导致了内部BLAST管道的开发，评估了储存库中sORF之间的序列相似性。在sORFs.org最初版本的概念模型证明的基础上，现在发布了完整的PRIDE-ReSpin管道，重新处理公开的基于MS的蛋白质组学PRIDE数据集，报告真实的翻译事件。除了报告这些识别的肽，sORFs.org还允许在Lorikeet MS/MS查看器中对注释的光谱进行目视检查，从而实现详细的手动检查和解释。
sORFs.org (http://www.sorfs.org) is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq). This update elaborates on the major improvements implemented since its initial release. sORFs.org now additionally supports three more species (zebrafish, rat and Caenorhabditis elegans) and currently includes 78 RIBO-seq datasets, a vast increase compared to the three that were processed in the initial release. Therefore, a novel pipeline was constructed that also enables sORF detection in RIBO-seq datasets comprising solely elongating RIBO-seq data while previously, matching initiating RIBO-seq data was necessary to delineate the sORFs. Furthermore, a novel noise filtering algorithm was designed, able to distinguish sORFs with true ribosomal activity from simulated noise, consequently reducing the false positive identification rate. The inclusion of other species also led to the development of an inner BLAST pipeline, assessing sequence similarity between sORFs in the repository. Building on the proof of concept model in the initial release of sORFs.org, a full PRIDE-ReSpin pipeline was now released, reprocessing publicly available MS-based proteomics PRIDE datasets, reporting on true translation events. Next to reporting those identified peptides, sORFs.org allows visual inspection of the annotated spectra within the Lorikeet MS/MS viewer, thus enabling detailed manual inspection and interpretation.
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DOI：
10.1093/bioinformatics/btr209
发表时间：
2011-07-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Lin MF;Jungreis I;Kellis M
通讯作者：
Kellis M
影响因子：
1.7
作者：
Siepel, A;Haussler, D
通讯作者：
Haussler, D
影响因子：
9.5
作者：
Hao, Yajing;Zhang, Lili;Chen, Runsheng
通讯作者：
Chen, Runsheng
影响因子：
4
作者：
Pauli, Andrea;Valen, Eivind;Schier, Alexander F.
通讯作者：
Schier, Alexander F.
影响因子：
14.9
作者：
Dinkel H;Van Roey K;Michael S;Kumar M;Uyar B;Altenberg B;Milchevskaya V;Schneider M;Kühn H;Behrendt A;Dahl SL;Damerell V;Diebel S;Kalman S;Klein S;Knudsen AC;Mäder C;Merrill S;Staudt A;Thiel V;Welti L;Davey NE;Diella F;Gibson TJ
通讯作者：
Gibson TJ