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n***w
发帖数: 2405 | 4 Hi, all,
I have a simple question but I do not know the solution...
I am trying to figure out how to do multiple sequence alignment using the
online tool from EMBL.
I always get the warning from the 1st step that at least two sequences are
needed...
I do not know how to fix this since I already put two sequences...
Probably I used the wrong format for that.
Thank you all... |
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A********0
发帖数: 3310 | 5 你有没有用对 file's format?
It works well to me. |
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n***w
发帖数: 2405 | 6 That's probably the thing...
Would you mind sending me a sample file? Thank you... |
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n***w
发帖数: 2405 | 7 That's probably the thing...
Would you mind sending me a sample file? Thank you... |
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l*****a
发帖数: 1431 | 8 did you put > at the beginning of each sequencing? It should be like this
>name1
sequence1
>name2
sequence2
.... |
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A********0
发帖数: 3310 | 9 correct. or try this.
>A.DE.x.IFA86_Z30637
ATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAGGTAGACAGGATGAG
GATTAGAACATGGAACAGTTTAGTAAAACATCATATGTATGTCTCTAAGA
AAGCTAAGGGTTGGTTTTATAGACATCACTTTGAATGTAGGCATCCAAAA
GCAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTAGTAGTAAG
AACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCACTTGGGTCAGG
GGGTCTCCATAGAATGGAGGCAGAAAAGATATAGCACACAAGTAGATCCT
GACCTAGCAGACCAACTGATTCACCTGCATTATTTTGACTGTTTTTCAGA
CTCTGCCATAAGGAAAGCCATATTAGGAGAAGTAGTTAGACCTAGGTGTG
AATATCAAGCAGGACATAACAAGGTAGGATCACTGCAATATTTGGCACT... 阅读全帖 |
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n***w
发帖数: 2405 | 10 Thank you all!!!
It worked!!! |
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n***w
发帖数: 2405 | 13 Blast align就可以了吧。
ClustalW2也可以。 |
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s********9
发帖数: 132 | 15 而且VMD是免费的.pymol现在收费了.
再问下:
1:homology model用哪个好? SPDV可以,不知道哪个好些? 文献上面说的homology的定量(比
如40% 60%是怎么来的? 是根据structural seq alignment 数完全相同的氨基酸数量除以总
数?还是别的?clustalw2是不给量化结果的.)
2:1)关于氢键,做结构的人文章里面到底donor atom 和acceptor atom离多远才算是可信? 我
前面用spdv似乎是定在3.5A.可是看一个文章里面描述的一个结构里面所谓重要的氢键已经4A以上
了.
2)一般说是N(O)-H...N(O),可是又看到有的文章里面说说C-H...N(o),这个氢键难道就是个
任人打扮的小姑娘?
3)如果在结构里面看到某个氨基酸的side chain和别的氨基酸有H bond,而我打算mutate这个
amino acids,一个结构生物学的人会怎么去推测这个mutation whether or to what
extent will affect the overall structure o... 阅读全帖 |
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A********0
发帖数: 3310 | 16 不熟悉这个网页。
不过很多软件都有类似功能。如果你真没办法在这个网页得到你想要的东西，用别的软
件试试。现在好东西很多，没必要在一棵树上吊死。 |
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b******n
发帖数: 4225 | 17 试了将对比的文件.aln下载下来用bioedit处理
好像能达到目的 |
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