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Weights for data related by a tree 总被引:8,自引:0,他引:8
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. 相似文献
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Gap costs for multiple sequence alignment 总被引:6,自引:0,他引:6
S F Altschul 《Journal of theoretical biology》1989,138(3):297-309
Standard methods for aligning pairs of biological sequences charge for the most common mutations, which are substitutions, deletions and insertions. Because a single mutation may insert or delete several nucleotides, gap costs that are not directly proportional to gap length are usually the most effective. How to extend such gap costs to alignments of three or more sequences is not immediately obvious, and a variety of approaches have been taken. This paper argues that, since gap and substitution costs together specify optimal alignments, they should be defined using a common rationale. Specifically, a new definition of gap costs for multiple alignments is proposed and compared with previous ones. Since the new definition links a multiple alignment's cost to that of its pairwise projections, it allows knowledge gained about two-sequence alignments to bear on the multiple alignment problem. Also, such linkage is a key element of recent algorithms that have rendered practical the simultaneous alignment of as many as six sequences. 相似文献
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Isolation of edestin from aleurone grains of Cannabis sativa 总被引:3,自引:0,他引:3
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Spherosomes of cotyledons of germinating peanuts (Arachis hypogea L.) were examined by electron microscopy and found to be particles about 1.0 to 2.0 μ in diameter bounded by a limiting membrane. Isolated spherosomes appear similar to spherosomes in situ. The isolated spherosomes are composed of 98.1% total lipids, 0.77% phospholipid and 1.27% protein by dry weight. The amounts of protein and phospholipid associated with the isolated spherosomes are sufficient to account for limiting membranes. Spherosomes amply account for the lipid in a peanut cotyledon. The activity of lipase and fatty acyl-Coenzyme A synthetase is not associated with the isolated spherosomes. This suggests that peanut spherosomes are principal sites of lipid storage but not of lipid degradation. 相似文献
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Most pairwise and multiple sequence alignment programs seek alignments with optimal scores. Central to defining such scores is selecting a set of substitution scores for aligned amino acids or nucleotides. For local pairwise alignment, substitution scores are implicitly of log-odds form. We now extend the log-odds formalism to multiple alignments, using Bayesian methods to construct “BILD” (“Bayesian Integral Log-odds”) substitution scores from prior distributions describing columns of related letters. This approach has been used previously only to define scores for aligning individual sequences to sequence profiles, but it has much broader applicability. We describe how to calculate BILD scores efficiently, and illustrate their uses in Gibbs sampling optimization procedures, gapped alignment, and the construction of hidden Markov model profiles. BILD scores enable automated selection of optimal motif and domain model widths, and can inform the decision of whether to include a sequence in a multiple alignment, and the selection of insertion and deletion locations. Other applications include the classification of related sequences into subfamilies, and the definition of profile-profile alignment scores. Although a fully realized multiple alignment program must rely upon more than substitution scores, many existing multiple alignment programs can be modified to employ BILD scores. We illustrate how simple BILD score based strategies can enhance the recognition of DNA binding domains, including the Api-AP2 domain in Toxoplasma gondii and Plasmodium falciparum. 相似文献
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