ArticleNature protocols2008
Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments.
Article in Nature protocols, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 75 citations in OpenAlex.
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- miR-122 and Ago interactions with the HCV genome alter the structure of the viral 5' terminus.Nucleic acids research · 2019Article
- Structure-Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch.ACS chemical biology · 2018Article
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- Coupling Green Fluorescent Protein Expression with Chemical Modification to Probe Functionally Relevant Riboswitch Conformations in Live Bacteria.Biochemistry · 2018Article
- Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis.Nature communications · 2018Article
- Concerted action of two 3' cap-independent translation enhancers increases the competitive strength of translated viral genomes.Nucleic acids research · 2017Article
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- Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
7 authors at 5 institutions in 1 country.
Funding
Abstract
We have developed protocols for rapidly quantifying the band intensities from nucleic acid chemical mapping gels at single-nucleotide resolution. These protocols are implemented in the software SAFA (semi-automated footprinting analysis) that can be downloaded without charge from http://safa.stanford.edu. The protocols implemented in SAFA have five steps: (i) lane identification, (ii) gel rectification, (iii) band assignment, (iv) model fitting and (v) band-intensity normalization. SAFA enables the rapid quantitation of gel images containing thousands of discrete bands, thereby eliminating a bottleneck to the analysis of chemical mapping experiments. An experienced user of the software can quantify a gel image in approximately 20 min. Although SAFA was developed to analyze hydroxyl radical (*OH) footprints, it effectively quantifies the gel images obtained with other types of chemical mapping probes. We also present a series of tutorial movies that illustrate the best practices and different steps in the SAFA analysis as a supplement to this protocol.
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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.