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Literature DB >> 15130839

Consensus sequence Zen.

Abstract

Consensus sequences are widely used in molecular biology but they have many flaws. As a result, binding sites of proteins and other molecules are missed during studies of genetic sequences and important biological effects cannot be seen. Information theory provides a mathematically robust way to avoid consensus sequences. Instead of using consensus sequences, sequence conservation can be quantitatively presented in bits of information by using sequence logo graphics to represent the average of a set of sites, and sequence walker graphics to represent individual sites.

Mesh：

Substances：
DNA, Bacterial

Year: 2002 PMID： 15130839 PMCID： PMC1852464

Source DB: PubMed Journal: Appl Bioinformatics ISSN： 1175-5636

38 in total

1. Sequence-specific recognition of double helical nucleic acids by proteins.

Authors: N C Seeman; J M Rosenberg; A Rich
Journal: Proc Natl Acad Sci U S A Date: 1976-03 Impact factor: 11.205

Review 2. Base flipping.

Authors: R J Roberts; X Cheng
Journal: Annu Rev Biochem Date: 1998 Impact factor: 23.643

3. Cells in temporal cortex of conscious sheep can respond preferentially to the sight of faces.

Authors: K M Kendrick; B A Baldwin
Journal: Science Date: 1987-04-24 Impact factor: 47.728

4. The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.

Authors: K M Reinisch; L Chen; G L Verdine; W N Lipscomb
Journal: Cell Date: 1995-07-14 Impact factor: 41.582

5. Information content of individual genetic sequences.

Authors: T D Schneider
Journal: J Theor Biol Date: 1997-12-21 Impact factor: 2.691

6. Information analysis of human splice site mutations.

Authors: P K Rogan; B M Faux; T D Schneider
Journal: Hum Mutat Date: 1998 Impact factor: 4.878

7. Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites.

Authors: R M Stephens; T D Schneider
Journal: J Mol Biol Date: 1992-12-20 Impact factor: 5.469

8. Information analysis of sequences that bind the replication initiator RepA.

Authors: P P Papp; D K Chattoraj; T D Schneider
Journal: J Mol Biol Date: 1993-09-20 Impact factor: 5.469

9. The promoter of the tgt/sec operon in Escherichia coli is preceded by an upstream activation sequence that contains a high affinity FIS binding site.

Authors: R K Slany; H Kersten
Journal: Nucleic Acids Res Date: 1992-08-25 Impact factor: 16.971

10. Mutational analysis of a prokaryotic recombinational enhancer element with two functions.

Authors: P Hübner; W Arber
Journal: EMBO J Date: 1989-02 Impact factor: 11.598

35 in total

1. Molecular flip-flops formed by overlapping Fis sites.

Authors: Paul N Hengen; Ilya G Lyakhov; Lisa E Stewart; Thomas D Schneider
Journal: Nucleic Acids Res Date: 2003-11-15 Impact factor: 16.971

Review 2. Consensus sequence Zen.

Authors: Thomas D Schneider
Journal: Appl Bioinformatics Date: 2002

Consensus sequence Zen.

1. Sequence-specific recognition of double helical nucleic acids by proteins.

Review 2. Base flipping.

3. Cells in temporal cortex of conscious sheep can respond preferentially to the sight of faces.

4. The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.

5. Information content of individual genetic sequences.

6. Information analysis of human splice site mutations.

7. Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites.

8. Information analysis of sequences that bind the replication initiator RepA.

9. The promoter of the tgt/sec operon in Escherichia coli is preceded by an upstream activation sequence that contains a high affinity FIS binding site.

10. Mutational analysis of a prokaryotic recombinational enhancer element with two functions.

1. Molecular flip-flops formed by overlapping Fis sites.

Review 2. Consensus sequence Zen.

3. TRII: A Probabilistic Scoring of Drosophila melanogaster Translation Initiation Sites.

4. Monomerization of far-red fluorescent proteins.

5. G-language genome analysis environment with REST and SOAP web service interfaces.

6. Effects of splicing mutations on NF2-transcripts: transcript analysis and information theoretic predictions.

7. Discovery and validation of information theory-based transcription factor and cofactor binding site motifs.

8. Hierarchy and feedback in the evolution of the Escherichia coli transcription network.

Review 9. Noncoding Variants Functional Prioritization Methods Based on Predicted Regulatory Factor Binding Sites.

10. Protein-precursor tRNA contact leads to sequence-specific recognition of 5' leaders by bacterial ribonuclease P.