| 查看: 544 | 回复: 3 | |||
| 当前主题已经存档。 | |||
[交流]
关于BLAST的用法！
|
|||
|
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！ |
回复此楼» 猜你喜欢
材料求调剂一志愿哈工大324
已经有5人回复
-
一志愿哈尔滨工业大学材料与化工方向336分
已经有5人回复
-
0856材料化工调剂 总分330
已经有9人回复
-
085602 化工专硕 338分 求调剂
已经有9人回复
-
352分 化工与材料
已经有4人回复
-
求调剂
已经有8人回复
-
材料求调剂 一志愿哈工大总分298分，前三科223分
已经有3人回复
-
085600 286分 材料求调剂
已经有4人回复
-
求调剂
已经有7人回复
-
275求调剂
已经有10人回复
playboy723
金虫 (正式写手)
- 应助: 0 (幼儿园)
- 金币: 783.3
- 帖子: 352
- 在线: 43.3小时
- 虫号: 344753
- 注册: 2007-04-14
- 性别: GG
- 专业: 遗传学和分子生物学
2楼2008-07-23 22:07:15
|
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
