In these days of facile cloning and rapid DNA sequencing, it is not uncommon for investigators to find themselves with a DNA sequence that may or may not code for a known gene product. The sequence is 'open' when read in an appropriate frame, which is to say that there is a long run of amino acid codons before the appearance of a terminator codon. How can we find out if this 'unidentified reading frame' (URF) really codes for a genuine protein, and how can we identify it if it exists? There are two general strategies, both of which can also be applied to the characterization of any 'open reading frame' (ORF), whether or not it has been 'identified'. The first and simplest approach involves computer searching and analysis; the second employs antibodies raised against synthetic peptides patterned on the sequence of the expected gene product. Both methods have been used with great success by many investigators. Each has, nonetheless, its pitfalls and frustrations. This primer is meant to guide the researcher past those obstacles as much as possible. Graduate students and researchers interested in amino acid sequencing; molecular biologists, biochemists, chemists, and biotechnologists.
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About the Author
Russell F. Doolittle is a Professor at the University of California, San Diego
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2 of 2 people found the following review helpful:
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A must for anyone dealing with biological sequence analysis.,
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This review is from: Of Urfs and Orfs: A Primer on How to Analyze Derived Amino Acid Sequences (Paperback)
This book will take you through the basic concepts of sequence analysis. Basic concepts of bioinformatics and sequence analysis are explained in a way any biologists can understand. This is a must if you ever compared two sequences or screened the database for homologous sequences (or if you ever intend to)
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Inside This Book
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First Sentence:
The first thing to find out about an open reading frame - an "orf" or "urf" - is, whether the sequence or something resembling it has already been reported. Read the first page Key Phrases - Statistically Improbable Phrases (SIPs): (learn more)
alignment score, coupling peptides, hydropathy profile, significant match, difference matrix, free peptide, optimal alignment, protein carrier New!
Books on Related Topics | Concordance | Text Stats Browse Sample Pages:
Front Cover | Table of Contents | First Pages | Index | Back Cover | Surprise Me!
The first thing to find out about an open reading frame - an "orf" or "urf" - is, whether the sequence or something resembling it has already been reported. Read the first page Key Phrases - Statistically Improbable Phrases (SIPs): (learn more)
alignment score, coupling peptides, hydropathy profile, significant match, difference matrix, free peptide, optimal alignment, protein carrier New!
Books on Related Topics | Concordance | Text Stats Browse Sample Pages:
Front Cover | Table of Contents | First Pages | Index | Back Cover | Surprise Me!
Citations (learn more)
This book cites 3
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7
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- Atlas of Protein Sequence and Structure (Vol 5, Supplement 3) by Margaret O. Dayhoff on page 4, Back Matter (1), and Back Matter (2)
- Genetic Engineering (Opposing Viewpoints) by Greenhaven Press in Back Matter
- Genetic Engineering: Principles and Methods by Jane K. Setlow in Back Matter
- Biomembrane Transport by Lon J. Van Winkle in Back Matter
- Naked Science: Anthropological Inquiry into Boundaries, Power, and Knowledge by Laura Nader in Back Matter
- Sequence - Evolution - Function: Computational Approaches in Comparative Genomics by Eugene V. Koonin in Back Matter
- International Review of Cytology, Volume 206 (International Review of Cell and Molecular Biology) by Kwang W. Jeon on page 3
- Fructose-2,6-Bisphosphate by Simon J. Pilkis on page 159
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