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  • BLAST search main parameters
    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 EXPECT threshold the match will not be reported Lower EXPECT thresholds are more stringent leading to fewer chance matches being reported Fractional values are acceptable See parameter E in the BLAST Manual CUTOFF Cutoff score for reporting high scoring segment pairs The default value is calculated from the EXPECT value see above HSPs are reported for a database sequence only if the statistical significance ascribed to them is at least as high as would be ascribed to a lone HSP having a score equal to the CUTOFF value Higher CUTOFF values are more stringent leading to fewer chance matches being reported See parameter S in the BLAST Manual Typically significance thresholds can be more intuitively managed using EXPECT MATRIX Specify an alternate scoring matrix for BLASTP BLASTX TBLASTN and TBLASTX The default matrix is BLOSUM62 Henikoff Henikoff 1992 The valid alternative choices include PAM40 PAM120 PAM250 and IDENTITY No alternate scoring matrices are available for BLASTN specifying the MATRIX directive in BLASTN requests returns an error response STRAND Restrict a TBLASTN search to just the top or bottom strand of the database sequences or restrict a BLASTN BLASTX or TBLASTX search to just reading frames on the top or bottom strand of the query sequence FILTER Mask off segments of the query sequence that have low compositional complexity as determined by the SEG program of Wootton Federhen Computers and Chemistry 1993 or segments consisting of short periodicity internal repeats as determined by the XNU program of Claverie States Computers and Chemistry 1993 or for BLASTN by the DUST program of Tatusov and Lipman in preparation Filtering can eliminate statistically significant but biologically uninteresting

    Original URL path: http://soybase.org/GlycineBlastPages/docs/options.html (2016-04-30)
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  • BLAST Color schema description
    color Similarity shown in blue color Mismatches shown in black color Color schema 4 No middle line Masked regions in lower case gray letters Everything else in upper case Unaligned regions in italic Identity shown in blue color Similarity shown in brown color Mismatches shown in red color Color schema 5 No middle line Masked regions in lower case gray letters Everything else in upper case Unaligned regions in italic

    Original URL path: http://soybase.org/GlycineBlastPages/docs/color_schema.html (2016-04-30)
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  • SoyCyc Database
    initio methods from the Gm1 01 Glycine max Williams82 genome sequence gene calls from the Joint Genome Institute JGI Phytozome The first step in using the program is to select a database using the selector at the top right of the page Clicking on change will drop down a selector window with a list of the available databases The choices are Database Name Description Glycine Max The SoyCyc Database Plant Metabolic Network Rhee Lab Medicago truncatula The MedicCyc Database Noble Foundation Sumner Lab PlantCyc Compendium of all public plant pathways Plant Metabolic Network Rhee Lab After highlighting your choice click the OK button in the lower right of the window The second step is to choose an activity from the menu bar above The Search button allows you to search for information in a number of ways Search By Description Compounds Searches using compound names Genes Proteins RNAs Searches using gene protein or structural RNA names Reactions Searches using biochemical reaction names Pathways Searches using proper pathway names Advanced Perform direct database queries Ontologies Search for genes and pathway information using ontological terms from GO EC etc The Tools button allows you access to a number of computational tools to

    Original URL path: http://soybase.org:8082/ (2016-04-30)
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