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166 7 Sequence Similarity Searching Tools like DNA, a protein must fold into a functionally competent 3D structure. Summary In ...

7.4 BLAST 167 Figure 7.3 Comparison of the extreme value distribution with the normal distribu- tion. distinct HSPs that would h ...

168 7 Sequence Similarity Searching Tools E-value P-value 10 0.9999546 5 0.9932621 1 0.6321206 0.1 0.0951626 0.05 0.0487706 0.00 ...

7.4 BLAST 169 Another difference is that the result of a PSSM search can be expressed in terms of the probability that a type of ...

170 7 Sequence Similarity Searching Tools search. The disadvantage of PHI-BLAST is that it is designed to combine pattern search ...

7.4 BLAST 171 that have been conserved by evolution (Kelley et al. 2004). The basic method searches for high-scoring alignments ...

172 7 Sequence Similarity Searching Tools genome likely to be homologous to the query sequence. It performs an align- ment betwe ...

7.4 BLAST 173 Figure 7.5 BLAT output window. MPBLAST: sets of small queries; MegaBLAST: greedy algorithm; WU-BLAST2: new versio ...

174 7 Sequence Similarity Searching Tools 7.5 Exercises Ifm= 100andn= 120, 000 , 000 , what normalized bit scoreS′is necessary ...

8 Query Languages For relational databases the standard query language is SQL. The main pur- pose of SQL is to select records fr ...

176 8 Query Languages 8.1 XML Navigation Using XPath XPath is a language for selecting parts of an XML document (W3C 1999). If o ...

8.1 XML Navigation Using XPath 177 //Chemical/* attribute. To select an attribute, use an@followed by the name of the attribute ...

178 8 Query Languages While directory paths and XML paths are very similar, there is a distinction mentioned in table 1.1 which ...

8.1 XML Navigation Using XPath 179 sum(set) Sum of a set of matching elements or attributes count(set) Number of matching elemen ...

180 8 Query Languages The XPath language is already a versatile query language. However, it is not a general query or transforma ...

8.2 Querying XML Using XQuery 181 will return all of the interview records in the health study database. Alternatively, one can ...

182 8 Query Languages for $bmi in document("healthstudy.xml")//Interview/@BMI where $bmi > 30 return $bmi Thereturnclause cor ...

8.3 Semantic Web Queries 183 for $desc in document("medline.xml")//MeshHeading/DescriptorName let $cite := ../../MedlineCitation ...

184 8 Query Languages A language based on rule engines. As we noted in section 3.1, a query is just a rule with no conclusion, ...

8.4 Exercises 185 Given a BioML document as in figure 1.3, find all literature references for the insulin gene. In the PubMed d ...