ArticleNucleic acids research2010
SEWAL: an open-source platform for next-generation sequence analysis and visualization.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed.
- Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology.International journal of molecular sciences · 2020Review
- Time-lapse imaging of molecular evolution by high-throughput sequencing.Nucleic acids research · 2018Article
- Applications of High-Throughput Sequencing for In Vitro Selection and Characterization of Aptamers.Pharmaceuticals (Basel, Switzerland) · 2016Review
- In vitro evolution of coenzyme-independent variants from the glmS ribozyme structural scaffold.Methods (San Diego, Calif.) · 2016Article
- Computational analysis of fitness landscapes and evolutionary networks from in vitro evolution experiments.Methods (San Diego, Calif.) · 2016Article
- FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections.Molecular therapy. Nucleic acids · 2015Article
- Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.GigaScience · 2015Review
- High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase.Nucleic acids research · 2013Article
- Fitness analyses of all possible point mutations for regions of genes in yeast.Nature protocols · 2012Article
- Deep mutational scanning: assessing protein function on a massive scale.Trends in biotechnology · 2011Review
- Rapid construction of empirical RNA fitness landscapes.Science (New York, N.Y.) · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Next-generation DNA sequencing platforms provide exciting new possibilities for in vitro genetic analysis of functional nucleic acids. However, the size of the resulting data sets presents computational and analytical challenges. We present an open-source software package that employs a locality-sensitive hashing algorithm to enumerate all unique sequences in an entire Illumina sequencing run (∼ 10(8) sequences). The algorithm results in quasilinear time processing of entire Illumina lanes (∼ 10(7) sequences) on a desktop computer in minutes. To facilitate visual analysis of sequencing data, the software produces three-dimensional scatter plots similar in concept to Sewall Wright and John Maynard Smith's adaptive or fitness landscape. The software also contains functions that are particularly useful for doped selections such as mutation frequency analysis, information content calculation, multivariate statistical functions (including principal component analysis), sequence distance metrics, sequence searches and sequence comparisons across multiple Illumina data sets. Source code, executable files and links to sample data sets are available at http://www.sourceforge.net/projects/sewal.
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Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.