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Literature DB >> 2760928

Weights for data related by a tree.

Abstract

How can one characterize a set of data collected from different biological species, or indeed any set of data related by an evolutionary tree? The structure imposed by the tree implies that the data are not independent, and for most applications this should be taken into account. We describe strategies for weighting the data that circumvent some of the problems of dependency.

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Year: 1989 PMID： 2760928 DOI： 10.1016/0022-2836(89)90234-9

Source DB: PubMed Journal: J Mol Biol ISSN： 0022-2836 Impact factor: 5.469

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Cited

31 in total

Review 1. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.

Authors: A A Schäffer; L Aravind; T L Madden; S Shavirin; J L Spouge; Y I Wolf; E V Koonin; S F Altschul
Journal: Nucleic Acids Res Date: 2001-07-15 Impact factor: 16.971

2. Contact-based sequence alignment.

Authors: Jens Kleinjung; John Romein; Kuang Lin; Jaap Heringa
Journal: Nucleic Acids Res Date: 2004-04-30 Impact factor: 16.971

3. An assessment of substitution scores for protein profile-profile comparison.

Authors: Xugang Ye; Guoli Wang; Stephen F Altschul
Journal: Bioinformatics Date: 2011-10-13 Impact factor: 6.937

4. ProbCons: Probabilistic consistency-based multiple sequence alignment.

Authors: Chuong B Do; Mahathi S P Mahabhashyam; Michael Brudno; Serafim Batzoglou
Journal: Genome Res Date: 2005-02 Impact factor: 9.043

5. A survey of multiple sequence comparison methods.

Authors: S C Chan; A K Wong; D K Chiu
Journal: Bull Math Biol Date: 1992-07 Impact factor: 1.758

6. Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity.

Authors: Eric A Stone; Arend Sidow
Journal: Genome Res Date: 2005-06-17 Impact factor: 9.043

Weights for data related by a tree.

Review 1. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.

2. Contact-based sequence alignment.

3. An assessment of substitution scores for protein profile-profile comparison.

4. ProbCons: Probabilistic consistency-based multiple sequence alignment.

5. A survey of multiple sequence comparison methods.

6. Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity.

7. The relative inefficiency of sequence weights approaches in determining a nucleotide position weight matrix.

8. Graemlin: general and robust alignment of multiple large interaction networks.

9. Multiple sequence alignment by conformational space annealing.

10. A phylogenetic approach for weighting genetic sequences.