Information content of individual genetic sequences

Journal of Theoretical Biology
T D Schneider

Abstract

Related genetic sequences having a common function can be described by Shannon's information measure and depicted graphically by a sequence logo. Though useful for many purposes, sequence logos only show the average sequence conservation, and inferring the conservation for individual sequences is difficult. This limitation is overcome by the individual information ( R i) technique described here. The method begins by generating a weight matrix from the frequencies of each nucleotide or amino acid at each position of the aligned sequences. This matrix is then applied to the sequences themselves to determine the sequence conservation of each individual sequence. The matrix is unique because the average of these assignments is the total sequence conservation, ad there is only one way to construct such a matrix. For binding sites on polynucleotides, the weight matrix has a natural cut off that distinguishes functional sequences from other sequences. R i values are on an absolute scale measured in bits of information so the conservation of different biological functions can be compared with one another. The matrix can be used to rank-order the sequences, to search for new sequences, to compare sequences to other quantitative data su...Continue Reading

Citations

Sep 4, 2009·Journal of Biological Physics·Xiao-Zhou ChenCi-Quan Liu
Aug 21, 2013·Nature Genetics·Arun S RajkumarSebastian J Maerkl
Dec 19, 2009·Proceedings of the National Academy of Sciences of the United States of America·Josh T CuperusJames C Carrington
Nov 17, 2005·Bioinformatics·J J GordonP Timms
Sep 8, 2010·Bioinformatics·A Robbins-PiankaM P Weir
Dec 17, 2010·Bioinformatics·Melissa S Cline, Rachel Karchin
Jul 25, 2000·Nucleic Acids Research·T D Schneider
Nov 7, 2003·Nucleic Acids Research·Paul N HengenThomas D Schneider
Sep 25, 2004·Nucleic Acids Research·Chengpeng Bi, Peter K Rogan
Dec 26, 2006·Nucleic Acids Research·Ryan K ShultzabergerThomas D Schneider
Jul 10, 2007·Nucleic Acids Research·Ryan K ShultzabergerThomas D Schneider
Oct 9, 2007·Nucleic Acids Research·Zehua ChenThomas D Schneider
May 23, 2008·Nucleic Acids Research·Ilya G LyakhovThomas D Schneider
Jun 10, 2011·Nucleic Acids Research·Santosh ChauhanJaya Sivaswami Tyagi
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Mar 17, 2009·Applied and Environmental Microbiology·Sonia BañosPaloma Liras
Sep 18, 2004·Journal of Bacteriology·Elisabeth HärtigMichiko M Nakano
Jan 24, 2006·Journal of Bacteriology·Heike ReentsElisabeth Härtig
Nov 10, 2001·Annual Review of Genomics and Human Genetics·D B Searls
Feb 16, 2008·EURASIP Journal on Bioinformatics & Systems Biology·John S Conery
Feb 15, 2011·EURASIP Journal on Bioinformatics & Systems Biology·Michael P Weir, Michael D Rice
Feb 13, 2009·BMC Bioinformatics·Ivan Erill, Michael C O'Neill
Jun 9, 2012·BMC Bioinformatics·Laura J AnzaldiIvan Erill
Jun 29, 2012·BMC Bioinformatics·Amin Zia, Alan M Moses
Aug 24, 2005·BMC Bioinformatics·Deendayal DinakarpandianPeter K Rogan
Mar 1, 2006·BMC Bioinformatics·Chengpeng Bi, Peter K Rogan
Jan 6, 2009·BMC Bioinformatics·A K M A BatenB C H Chang

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.