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    Original URL path: http://soybase.org/GeneCallSearch/GeneCallSearch.php (2016-04-30)
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    Original URL path: /dlpages/index.php?seqdl= (2016-04-30)


  • Programs available for the BLAST search
    query sequence against a protein sequence database blastn compares a nucleotide query sequence against a nucleotide sequence database blastx compares a nucleotide query sequence translated in all reading frames against a protein sequence database tblastn compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames tblastx compares the six frame translations of a nucleotide query sequence against the six frame translations of a nucleotide

    Original URL path: http://soybase.org/GlycineBlastPages/docs/blast_program.html (2016-04-30)
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  • Low complexity filtering
    N in nucleotide sequence e g NNNNNNNNNNNNN and the letter X in protein sequences e g XXXXXXXXX Users may turn off filtering by using the Filter option on the Advanced options for the BLAST server page Reference for the DUST program Tatusov R L and D J Lipman in preparation Hancock J M and J S Armstrong 1994 SIMPLE34 an improved and enhanced implementation for VAX and Sun computers of

    Original URL path: http://soybase.org/GlycineBlastPages/docs/filtered.html (2016-04-30)
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  • BLAST search main parameters
    Fractional values are acceptable INCLUSION THRESHOLD The statistical significance threshold for including a sequence in the model used by PSI BLAST on the next iteration ORGANISM NAME Enter the organism name in the form Genus species e g Homo sapiens A number of popular organism names are listed on a pull down menu TAXONOMIC CLASSIFICATION Enter any taxonomic group from the NCBI taxonomy e g Mammalia Some popular groups are Archaea Bacteria Eukaryota Embryophyta higher plants Fungi Metazoa multicellular animals Vertebrata Mammalia Rodentia Primates Explore the taxonomy database at NCBI FILTER Low complexity 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 for BLASTN by the DUST program of Tatusov and Lipman in preparation Filtering can eliminate statistically significant but biologically uninteresting reports from the blast output e g hits against common acidic basic or proline rich regions leaving the more biologically interesting regions of the query sequence available for specific matching against database sequences Filtering is only applied to the query sequence or its translation products not to database sequences Default filtering is DUST for BLASTN SEG for other programs It is not unusual for nothing at all to be masked by SEG when applied to sequences in SWISS PROT so filtering should not be expected to always yield an effect Furthermore in some cases sequences are masked in their entirety indicating that the statistical significance of any matches reported against the unfiltered query sequence should be suspect FILTER Human repeats This option masks Human repeats LINE s and SINE s and is especially useful for human sequences that may contain these repeats This option is still experimental and under development so it may change in the near future FILTER Mask for

    Original URL path: http://soybase.org/GlycineBlastPages/docs/newoptions.html (2016-04-30)
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  • Matrix and Gap Costs
    any matrices with relative entropies suitable for the shortest queries so the older PAM matrices 5 6 may be used instead For proteins a provisional table of recommended substitution matrices and gap costs for various query lengths is Query length Substitution matrix Gap costs 85 BLOSUM 62 11 1 Gap Costs The raw score of an alignment is the sum of the scores for aligning pairs of residues and the scores for gaps Gapped BLAST and PSI BLAST use affine gap costs which charge the score a for the existence of a gap and the score b for each residue in the gap Thus a gap of k residues receives a total score of a bk specifically a gap of length 1 receives the score a b Lambda Ratio To convert a raw score S into a normalized score S expressed in bits one uses the formula S lambda S ln K ln 2 where lambda and K are parameters dependent upon the scoring system substitution matrix and gap costs employed 7 9 For determining S the more important of these parameters is lambda The lambda ratio quoted here is the ratio of the lambda for the given scoring system to that for one using the same substitution scores but with infinite gap costs 8 This ratio indicates what proportion of information in an ungapped alignment must be sacrificed in the hope of improving its score through extension using gaps We have found empirically that the most effective gap costs tend to be those with lambda ratios in the range 0 8 to 0 9 1 Altschul S F 1991 Amino acid substitution matrices from an information theoretic perspective J Mol Biol 219 555 565 2 States D J Gish W Altschul S F 1991 Improved sensitivity of nucleic acid

    Original URL path: http://soybase.org/GlycineBlastPages/docs/matrix_info.html (2016-04-30)
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  • Out-of-frame notation
    G T K F A T G G Q G Q D S GK V V TBO DGTKFATGGQGQDSG GVV DGTKFATGGQGQDSG VV DGTKFATGGQGQDSG KVV 2 1 nucletide missing frameshift 1 TBO notation OOF alignment with DNAP DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGGERGV D G T K F A T G G Q G Q D S G K V TBO DGTKFATGGQGQDS GEV DGTKFATGGQGQDS G V DGTKFATGGQGQDS GKV 3 Complete match OOF alignment with DNAP DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGGEKRGV D

    Original URL path: http://soybase.org/GlycineBlastPages/docs/oof_notation.html (2016-04-30)
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  • NCBI BLAST Advanced Options
    W Word size default is 11 for blastn 3 for other programs v Number of one line descriptions V Integer default 100 b Number of alignments to show B Integer default 100 BLASTP Program Advanced Options BLASTX Program Advanced Options TBLASTN Program Advanced Options G Cost to open a gap Integer default 11 E Cost to extend a gap Integer default 1 e Expectation value E Real default 10 0

    Original URL path: http://soybase.org/GlycineBlastPages/docs/full_options.html (2016-04-30)
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