l*****g
发帖数: 263 | 1 Could you please recommend a program for below purpose? Thanks.
I have a short (20-30 residues) protein sequence and I would like to find
the best matches on a long protein sequence (2000 residues). Can anyone
recommend a good program to handle this? It will be better if I can have a
list of matches on the long sequence with scores.
Now a bit difficult, I have a pattern, say DdGLLeqHLGGrgG (where capital
letters mean more conserved). I need to find the best match for this pattern
. Could someone recommend some program to do this as well?
Thanks a lot. |
i*****i
发帖数: 154 | 2 protein BLAST of NCBI
there is an option "Align two or more sequences"
it will use BLAST algorithm to search the similarity region between two
sequences instead of the protein database.
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&BLAST_PR |
l*****g
发帖数: 263 | 3 Thanks a lot.
How about the pattern search as I mentioned in the second paragraph?
BLAST does allow wild cards, but can't allow people to put weight on
individual search.
【在 i*****i 的大作中提到】
: protein BLAST of NCBI
: there is an option "Align two or more sequences"
: it will use BLAST algorithm to search the similarity region between two
: sequences instead of the protein database.
: http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&BLAST_PR
|
c********b
发帖数: 363 | 4 You may try FUGUE and get some leads if you are lucky.
Here is the link to explanation:
http://computing.bio.cam.ac.uk/local/doc/fugue-long.html
pattern
【在 l*****g 的大作中提到】
: Could you please recommend a program for below purpose? Thanks.
: I have a short (20-30 residues) protein sequence and I would like to find
: the best matches on a long protein sequence (2000 residues). Can anyone
: recommend a good program to handle this? It will be better if I can have a
: list of matches on the long sequence with scores.
: Now a bit difficult, I have a pattern, say DdGLLeqHLGGrgG (where capital
: letters mean more conserved). I need to find the best match for this pattern
: . Could someone recommend some program to do this as well?
: Thanks a lot.
|
g**********t
发帖数: 475 | 5 你的第二个问题可以用HMMER来做，行业标准。不过只有你的"pattern"是不够的，因为
你的"pattern"并没有精确给出"weights"。如果你的"pattern"是从一堆reference
sequences里面总结出来的，你可以直接把reference sequences的alignment喂给HMMER
，HMMER会生成一个customized hidden Markov model用来寻找匹配的序列。
http://hmmer.janelia.org/ |
l*****g
发帖数: 263 | 6 checking on this now ...
【在 c********b 的大作中提到】
: You may try FUGUE and get some leads if you are lucky.
: Here is the link to explanation:
: http://computing.bio.cam.ac.uk/local/doc/fugue-long.html
:
: pattern
|
l*****g
发帖数: 263 | 7 em. I feel this may be a better way to go.
Current question is: we know a binding pattern, and we wanted to know the
potential binding sites on a long sequence. Very traditional question.
Thanks and I will try it as well.
HMMER
【在 g**********t 的大作中提到】
: 你的第二个问题可以用HMMER来做，行业标准。不过只有你的"pattern"是不够的，因为
: 你的"pattern"并没有精确给出"weights"。如果你的"pattern"是从一堆reference
: sequences里面总结出来的，你可以直接把reference sequences的alignment喂给HMMER
: ，HMMER会生成一个customized hidden Markov model用来寻找匹配的序列。
: http://hmmer.janelia.org/
|
z*********8
发帖数: 1203 | 8
HMMER
这个hhpred 是不是跟你说的一样啊？？http://toolkit.tuebingen.mpg.de/hhpred
【在 g**********t 的大作中提到】
: 你的第二个问题可以用HMMER来做，行业标准。不过只有你的"pattern"是不够的，因为
: 你的"pattern"并没有精确给出"weights"。如果你的"pattern"是从一堆reference
: sequences里面总结出来的，你可以直接把reference sequences的alignment喂给HMMER
: ，HMMER会生成一个customized hidden Markov model用来寻找匹配的序列。
: http://hmmer.janelia.org/
|
A*****n
发帖数: 243 | 9 你这种情况用prosite最合适了
http://prosite.expasy.org/scanprosite/
pattern
【在 l*****g 的大作中提到】
: Could you please recommend a program for below purpose? Thanks.
: I have a short (20-30 residues) protein sequence and I would like to find
: the best matches on a long protein sequence (2000 residues). Can anyone
: recommend a good program to handle this? It will be better if I can have a
: list of matches on the long sequence with scores.
: Now a bit difficult, I have a pattern, say DdGLLeqHLGGrgG (where capital
: letters mean more conserved). I need to find the best match for this pattern
: . Could someone recommend some program to do this as well?
: Thanks a lot.
|
f*********e
发帖数: 24 | 10 Ctrl + F
在长序列里面 “查找”
pattern
【在 l*****g 的大作中提到】
: Could you please recommend a program for below purpose? Thanks.
: I have a short (20-30 residues) protein sequence and I would like to find
: the best matches on a long protein sequence (2000 residues). Can anyone
: recommend a good program to handle this? It will be better if I can have a
: list of matches on the long sequence with scores.
: Now a bit difficult, I have a pattern, say DdGLLeqHLGGrgG (where capital
: letters mean more conserved). I need to find the best match for this pattern
: . Could someone recommend some program to do this as well?
: Thanks a lot.
|
