Sequence context-specific profiles for homology searching
نویسندگان
چکیده
منابع مشابه
Sequence context-specific profiles for homology searching.
Sequence alignment and database searching are essential tools in biology because a protein's function can often be inferred from homologous proteins. Standard sequence comparison methods use substitution matrices to find the alignment with the best sum of similarity scores between aligned residues. These similarity scores do not take the local sequence context into account. Here, we present an ...
متن کاملSequence context-specific profiles for homology searching: Supplementary Information
Generation of context profile library N = 1 million training profiles of length l = 2d+1 were generated as described in the main text and Figure 2. Each training profile is represented by a count profile cn(j, x), which specifies the counts of amino acid x ∈ {1, . . . , 20} at position j ∈ {−d, . . . , d}. These counts are obtained by multiplying the sequence profile tn(j, x) by the effective n...
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Sequence similarity searching, typically with BLAST, is the most widely used and most reliable strategy for characterizing newly determined sequences. Sequence similarity searches can identify “homologous” proteins or genes by detecting excess similarity— statistically significant similarity that reflects common ancestry. This unit provides an overview of the inference of homology from signific...
متن کاملAn introduction to sequence similarity ("homology") searching.
Homologous sequences usually have the same, or very similar, functions, so new sequences can be reliably assigned functions if homologous sequences with known functions can be identified. Homology is inferred based on sequence similarity, and many methods have been developed to identify sequences that have statistically significant similarity. This unit provides an overview of some of the basic...
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Keyword searching while very successful in narrowing down the contents of the Web to the pertaining subset of information, has two primary drawbacks. First, the accuracy of the search is closely coupled with the choice of keywords. Second, keywords are limited in their expressibility. In particular, they fail to adequately capture the “contextual information” implicit in most searches done by u...
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ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 2009
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.0810767106