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146 6 Information Retrieval Summary Citations (such as hypertext links) can be used to rank documents relevant to a query accor ...

6.5 Vector Space Retrieval of Knowledge Representations 147 you can extract from them. Concept combination could be a powerful i ...

148 6 Information Retrieval such topics can be handled by an information retrieval system. Unlike ordi- nary terms, concept comb ...

6.6 Retrieval of Knowledge Representations 149 times the retrieval will be useless. These engines use a variety of mechanisms fo ...

150 6 Information Retrieval of every natural language statement. However, it is possible to extract know- ledge representations ...

6.6 Retrieval of Knowledge Representations 151 com. Figure 6.2 is an example of a query presented to SKIP. The query in this cas ...

152 6 Information Retrieval Figure 6.3 Top part of the result screen for the SKIP retrieval system showing the knowledge represe ...

6.6 Retrieval of Knowledge Representations 153 Figure 6.4 Other documents that match a query. The knowledge representations show ...

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7 Sequence Similarity Searching Tools Information retrieval can take many forms, and does not have to be based on natural langua ...

156 7 Sequence Similarity Searching Tools a way of lining up the residues in the query sequence with part of a sequence in the c ...

7.1 Basic Concepts 157 formula. Logarithms are used so that total scores can be computed by adding the scores for individual res ...

158 7 Sequence Similarity Searching Tools 10 log 10 units, which is roughly the same as third-bit units. BLOSUM matri- ces are u ...

7.3 FASTA 159 smaller and smaller problems until the smallest problems have trivial solu- tions. The smaller solutions are then ...

160 7 Sequence Similarity Searching Tools ktupis 2 for amino acid and 6 for nucleotide sequences. The next step is to extend the ...

7.4 BLAST 161 Summary FASTA is a set of sequence similarity search programs. FASTA is also a sequence format, and this is curre ...

162 7 Sequence Similarity Searching Tools Before discussing the algorithmic details of BLAST, it is helpful to mention some key ...

7.4 BLAST 163 is detected if it contains two nonoverlapping words of lengthWwhose scores are at least the thresholdT, with start ...

164 7 Sequence Similarity Searching Tools 7.4.2 BLAST Search Types BLAST can be used to perform the following types of sequence ...

7.4 BLAST 165 Figure 7.2 Illustration of blastx (version 2.2.10) output using a 718-bp DNA se- quence (GenBank accession number ...