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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
9
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pubmed:dateCreated |
2008-9-5
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pubmed:abstractText |
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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pubmed:grant |
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pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-10998234,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-11015228,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-11352576,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-11980483,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-12729738,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-12948483,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-15319447,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-15491606,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-15701734,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-15796531,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-16242711,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-16408007,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-16484377,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-16574145,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-16582097,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-17299128,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-17438287,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-2417197,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-2501870,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-2579378,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-3464963,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-7862644,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-9054977,
http://linkedlifedata.com/resource/pubmed/commentcorrection/18772866-9506944
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:status |
MEDLINE
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pubmed:issn |
1750-2799
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pubmed:author |
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pubmed:issnType |
Electronic
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pubmed:volume |
3
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
1395-401
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pubmed:dateRevised |
2011-9-26
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pubmed:meshHeading |
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pubmed:year |
2008
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pubmed:articleTitle |
Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments.
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pubmed:affiliation |
Department of Developmental Genetics and Bioinformatics, Wadsworth Center, Albany, New York 12208, USA. alain@wadsworth.org
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pubmed:publicationType |
Journal Article,
Research Support, U.S. Gov't, Non-P.H.S.,
Research Support, Non-U.S. Gov't,
Research Support, N.I.H., Extramural
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