Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
نویسندگان
چکیده
منابع مشابه
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships.
Pairwise sequence comparison methods have been assessed using proteins whose relationships are known reliably from their structures and functions, as described in the SCOP database [Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia C. (1995) J. Mol. Biol. 247, 536-540]. The evaluation tested the programs BLAST [Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). J. Mo...
متن کاملComparison of Sequence Similarity Measures for Distant Evolutionary Relationships
Sequence similarity algorithms are used to reconstruct increasing large evolutionary trees involving increasingly distant evolutionary relationships. This paper proposes two sequence similarity algorithms, called the Greedy Tiling and the Random Tiling algorithms, that are both based on the idea of tiling one sequence by parts of another sequence. Experimental comparisons show that the new algo...
متن کاملAssessing sequence comparison methods with the average precision criterion
MOTIVATION Comprehensive performance assessment is important for improving sequence database search methods. Sensitivity, selectivity and speed are three major yet usually conflicting evaluation criteria. The average precision (AP) measure aims to combine the sensitivity and selectivity features of a search algorithm. It can be easily visualized and extended to analyze results from a set of que...
متن کاملCritical assessment of structure-based sequence alignment methods at distant relationships
Accurate sequence alignments are crucial for modelling and to provide an evolutionary picture of related proteins. It is well-known that alignments are hard to obtain during distant relationships. Three thousand and fifty-two alignments of 218 pairs of protein domain structural entries, with <40% sequence identity, belonging to different structural classes, of diverse domain sizes and length-ri...
متن کاملevolutionary origin and phylogenetic relationships among fusarium oxysporum f. sp. melonis isolates in iran and their relationship with nonpathogenic isolates
پژمردگی فوزاریومی خربزه و طالبی با عامل fusarium oxysporum f. sp. melonis از بیماری های مهم قارچی در مناطق رشد این گیاهان می باشد. جدایه های f. oxysporum از گیاهان و خاک ریزوسفر متعلق به پنج استان مهم تولیدکننده ی خربزه و طالبی جداسازی شد و بر پایه ی بیماری زایی در ارقام افتراقی، گروه های سازگاری رویشی (vegetative compatibility groups)، توالی سنجی ناحیه ی جداکننده ی بین ژنی دی اِن اِی ریبوزومی (n...
15 صفحه اولذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 1998
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.95.11.6073