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关于BLAST的用法！
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各位路过的，有没有会用BLAST的，我现在正在做这个，但由于本科并不是学生物的，很多知识都不太懂，现在就卡在这个BLAST这里不会动了，谁会的教教我吧，我真的很感谢！ QQ：164186483 一般都在线上的，不过是隐身而已。 希望哪位大虾能一步步教一下，偶万分感谢啊！ |
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playboy723
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2楼2008-07-23 22:07:15
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Four components to a BLAST search (1) Choose the sequence (query) (2) Select the BLAST program (3) Choose the database to search (4) Choose optional parameters Step 1: Choose your sequence Sequence can be input in FASTA format or as accession number Step 2: Choose the BLAST program BLASTN - compares a nucleotide query to a nucleotide database BLASTP - compares a protein query to a protein 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 sequence database. Then click “BLAST” Step 3: choose the database nr = non-redundant (most general database) dbest = database of expressed sequence tags dbsts = database of sequence tag sites gss = genomic survey sequences htgs = high throughput genomic sequence BLAST: optional parameters You can... • choose the organism to search • turn filtering on/off • change the substitution matrix • change the expect (e) value • change the word size • change the output format Step 4a: Select optional search parameters About E-value the number of alignments with a given score S that would be expected to occur at random in the database that has been searched (e.g. if E=10, 10 matches with score S will be expected to be found by chance). A match will only be reported if its E value falls below the threshold set. Lower E thresholds are more stringent, and report fewer matches The key equation describing an E value is: E = Kmn e-lS This equation is derived from a description of the extreme value distribution S = the score E = the expect value = the number of HSPs expected to occur with a score of at least S m, n = the length of two sequences l, K = Karlin Altschul statistics Some properties of the equation E = Kmn e-lS The value of E decreases exponentially with increasing S (higher S values correspond to better alignments). Very high scores correspond to very low E values. Parameter K describes the search space (database). For E=1, one match with a similar score is expected to occur by chance. For a very much larger or smaller database, you would expect E to vary accordingly 希望对你有所帮助 |
3楼2008-07-24 12:25:58
4楼2008-07-24 17:03:03
