]> A predicate allowing any "thing" to assert a relationship to a HSP object. A predicate allowing any "thing" to assert a relationship to a ReferenceLibrary object. A predicate allowing any "thing" to assert a relationship to a ResultsSet object. A predicate allowing any "thing" to assert a relationship to a Sequence Service object. Normalized score for an alignment. Super property for all LIS datatype properties The sequence segment that may highlight matches, similar matches, or differences between the querySequence and subjectSequence. Should align base-for-base with the querySequence and the subjectSequence. The statistical significance threshold for reporting matches against database sequences; the default value is 10, such that 10 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the ExpectationThreshold, the match will not be reported. Lower Expectation thresholds are more stringent, leading to fewer chances matches being reported. Fractional values are acceptable. E-value The threshold above which BLAST will extend a hit found. The hit is based on finding a word of a certain size (see Word Size) This option masks Human repeats (LINE's, SINE's, plus retroviral repeasts) and is useful for human sequences that may contain these repeats. Filtering for repeats can increase the speed of a search especially with very long sequences (>100 kb) and against databases which contain large number of repeats (htgs). This filter should be checked for genomic queries to prevent potential problems that may arise from the numerous and often spurious matches to those repeat elements. Source: NCBI General parameters for filtering sequences. Cost to extend a gap, a 0 in this field means to use the default. Supported values for BLASTP, BLASTX, TBLASTN, and TBLASTX are limited. Cost to open a gap; a 0 in the field means to use the default. Supported values for BLASTP, BLASTX, TBLASTN, and TBLASTX are limited. General parameters for gapped alignments. Whether to allow gapped alignments; either ON or OFF. General parameters. Predicate to relate an object to another that has properties for HSP (High Scoring Pair) results. General and broadly used invocation parameters. Mask off--do not use--parts of the sequence with low information content (low compositional complexity). BLAST searches consist of two phases, finding hits based upon a lookup table and then extending them. This option masks only for purposes of constructing the lookup table used by BLAST so that no hits are found based upon low-complexity sequence or repeats (if repeat filter is checked). The BLAST extensions are performed without masking and so they can be extended through low-complexity sequence. Source: NCBI With this option selected you can cut and paste a FASTA sequence in upper case characters and denote areas you would like filtered with lower case. This allows you to customize what is filtered from the sequence during the comparison to the BLAST databases. Source: NCBI Maximum number of hits (sequence matches) to be returned by the service. See also maxScores and ExpectationThreshold. Maximum number of HSPs (High Scoring Pairs--also known as High scoring Segment Pairs and High scoring Sequence Pairs) for any given local alignment. See also maxAlignmentsReturned and ExpectationThreshold. keep lower upper aligned input Descriptive text or name for this set of parameters. Percent of matches that are identical. Percentage of amino acid matches that are chemical similar (but not necessarily identical). P-Value The sequence segment from the full sequence provided to the service for querying. Should align base-for-base with the subjectSequence and the (optional) differentialSequence. Descriptive text about the reference library. ID or identifying tag. Optional name. A URL to more information about the reference library. The version or build number of a database. Predicates used in the returning of results. General parameters setting the type of result to be returned. General parameters for determing the score associated with a HSP (High Scoring Pair). Invocation parameters associated with specific BLAST programs and implementations. Automatically adjust word size and other parameters to improve results for short queries. Source: NCBI The sequence segment as extracted from the reference database. Should align base-for-base with the querySequence and the (optional) differentialSequence. Tunning parameters (e.g., extension and expectation thresholds, word size, etc.). The size of the initial word that must be matched between the database and the query sequence. See http://blast.wustl.edu/blast/parameters.html See http://blast.wustl.edu/blast/parameters.html See http://blast.wustl.edu/blast/parameters.html See http://blast.wustl.edu/blast/parameters.html See http://blast.wustl.edu/blast/parameters.html See http://blast.wustl.edu/blast/parameters.html See http://blast.wustl.edu/blast/parameters.html See http://blast.wustl.edu/blast/parameters.html See http://blast.wustl.edu/blast/parameters.html NAR Webservers Subcategory from categories at http://www.oxfordjournals.org/nar/webservers/c See http://www.advbiocomp.com. Sequence comparison based on the the Basic Local Alignment Search Tool (BLAST) approach of: Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410. PubMed ID: 2231712. Popular implementations of BLAST programs. Query a nucleotide sequence against a library of nucleotide sequences Query an amino acid (protein) sequence against a library of amino acid (protein) sequences. Specific programs for sequence comparison based on the the Basic Local Alignment Search Tool (BLAST) approach of: Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410. PubMed ID: 2231712. Query an amino acid (protein) sequence against a library of amino acid (protein) sequences. A generic, semantically opaque BLAST Result; this acts as a marker class. Query 6-frame translations of a nucleotide sequence against a library of amino acid (protein) sequences. Specific programs for multiple sequence alignment based on ClustalW. A generic, semantically opaque ClustalW Result; this acts as a marker class. Sequence comparison approach of: Lipman DJ, Pearson WR 1985 Rapid and sensitive protein similarity searches.Science. Mar 22;227(4693):1435-41. PubMed ID: 2983426. http://www.ncbi.nlm.nih.gov/pubmed/2983426 DNA to DNA FASTA-family of programs. See: http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml http://en.wikipedia.org/wiki/Fasta Protein to protein A generic, semantically opaque FASTA Result; this acts as a marker class. DNA to protein 1 High Scoring Pair. Can be used to classify a sswap:Object with semantically tagged results from a BLAST search. See seqSvc:hspProperties. 0 0 Marker class for invocation objects for sequence services; i.e., sswap:Subjects or nodes associated with sswap:Subjects via a seqSvc:hasSequenceService predicate that have seqSvc:serviceSpecificParameters and seqSvc:invocationParameters. Faster BLASTN for multiple input sequences. See: Wheeler DL, Church DM, Federhen S, Lash E, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L. 2003 Database resources of the National Center for Biotechnology. Nucleic Acids Research, 2003, Vol. 31, No. 1 28-33. Source: http://nar.oxfordjournals.org/cgi/content/full/31/1/28 Faster BLASTN for multiple input sequences with non-contiguous word matching. See: Wheeler DL, Church DM, Federhen S, Lash E, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L. 2003 Database resources of the National Center for Biotechnology. Nucleic Acids Research, 2003, Vol. 31, No. 1 28-33. Source: http://nar.oxfordjournals.org/cgi/content/full/31/1/28 2 Mulitple Sequence Alignment invocation class See http://www.ncbi.nlm.nih.gov/BLAST NCBI BLAST version 1.0+ implementations. NCBI BLAST version 2.0+ implementations. Pattern Hit Initiated BLAST. Query an amino acid (protein) sequence against a library of amino acid (protein) sequences. "PHI-BLAST expects as input a protein query sequence and a pattern contained in that sequence. PHI-BLAST searches the specified database for other protein sequences that also contain the input pattern and have significant similarity to the query sequence in the vicinity of the pattern occurrences." Source: http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/Post_Blast.html. Position-Specific Iteration BLAST. Query an amino acid (protein) sequence against a library of amino acid (protein) sequences. More sensetive that BLASTP for detecting distantly related sequences. "Position specific iterative BLAST (PSI-BLAST) refers to a feature of BLAST 2.0 in which a profile (or position specific scoring matrix, PSSM) is constructed (automatically) from a multiple alignment of the highest scoring hits in an initial BLAST search." Source: http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/psi1.html 0 0 0 0 0 0 Marker class for reference libraries. 0 Marker class of 'Result objects' of sequence services. These are semantically opaque classes (i.e., they tag possibly complicated objects, the data of which is not individually tagged). These classes may be used to tag a resulting sswap:Object from a service. 1 0 Sequence Comparison invocation class Root class for all concepts Sequence comparison approach of: Smith TF, Waterman MS 1981 Identification of common molecular subsequences. J. Molec. Biol. 147: 195–197. Specific programs for sequence comparison based on the the Smith Waterman approach of: Smith TF, Waterman MS 1981 Identification of common molecular subsequences. J. Molec. Biol. 147: 195–197. A generic, semantically opaque Smith Waterman Result; this acts as a marker class. Query an amio acid (protein) sequence against a nucleotide library via 6-frame nucleotide translation. Query 6-frame translations of a nucleotide sequence against 6-frame translations from a library of nucleotide sequences. Specific programs for multiple sequence alignment based on tCoffee. A generic, semantically opaque tCoffee Result; this acts as a marker class. Protein to DNA Protein to DNA See http://blast.wustl.edu WU BLAST version 1.0+ implementations. WU BLAST version 1.0+ implementations.