How to find the repetitive elements of a sequence(NA or AA) - (Oct/23/2005 )
hi,
Could somebody tell me that :
1.How to find all the repetitive elements of a sequence(NA or AA)?(It means that the repetitive
elements of various length could be found out.)
Whether there is any software with which I can achieve it?
Mainly ,I want to find the single repetitive element which length is between 4 NA and 20 NA .
2.How to find the same elments (4NA<the length <20NA) between two seqences or among
several sequences?
Besides,when the elment in which 1 or 2 NA are variant is acceptable,how can I find all of
them.It means:
in one sequece ,the element is "TAGGCTT",
but in another seqence ,the element may be "TAGGCAT".
Try Repeat Masker at here http://www.repeatmasker.org/
Thanks!
I have not found the solution of "question 2".
Will the fuzznuc program of the Emboss package do what you want (see instructions here and a server here)? The FindPatterns program of GCG is similar, if you have that available.
Thank you very much!
Utilizing the "fuzznuc program" ,in a given long sequence,we can find all the candidates similary to the pattern which sequence is known clearly or comparatively ambiguously.
BUT,if I don't know the sequence of the pattern,how can I find the same(or 1-2 NA ambiguously) patterns between two long sequences or among more sequences?
Whether the "Cluster w" can do it?
Clustal is a global alignment tool, I don't think it'll do what you want (though, to be honest, I'm not entirely certain what it is you're trying to do)...
To find regions of similarity amongst many sequences, regardless of where they lie, perhaps MEME would be a better choice (see here). The emboss programs equicktandem, etandem, einverted, and palindrome might also be useful.
For example, some research I did (here) found a rcombinase that controlled expression of many genes by DNA inversion via inverted repeats that flanked the promoters. Once I had an example of the IRs, I used various programs like those I've listed to find other examples in the genome resembling the known IRs, and found six additional regions controlled in the same manner by the same recombinase.
Could somebody tell me that :
1.How to find all the repetitive elements of a sequence(NA or AA)?(It means that the repetitive
elements of various length could be found out.)
Whether there is any software with which I can achieve it?
Mainly ,I want to find the single repetitive element which length is between 4 NA and 20 NA .
2.How to find the same elments (4NA<the length <20NA) between two seqences or among
several sequences?
Besides,when the elment in which 1 or 2 NA are variant is acceptable,how can I find all of
them.It means:
in one sequece ,the element is "TAGGCTT",
but in another seqence ,the element may be "TAGGCAT".
1. repeat mask
2. regular expression, sth like TAGGC[A|T]T
Appreciate greatly for your advice!
using the "MEME program",I have uploaded several sequences to the web server for motif finding.The result will be sent to my email.
In order to using the "MEME"locally,whether there is the software which can be download?
Besides. I do not know how to use the " regular expression".How can I do it ?
using the "MEME program",I have uploaded several sequences to the web server for motif finding.The result will be sent to my email.
In order to using the "MEME"locally,whether there is the software which can be download?
Besides. I do not know how to use the " regular expression".How can I do it ?
A regular expression is generally something associated with programming... a language like perl or python.
Simply it allows you to define a pattern and search a string for that pattern.
my $string = "FOOBARATCGBARFOO";
if ($string =~ /ATCG/) { print "Pattern Found!\n";}
For an introduction see Beginning Perl for Bioinformatics by Tisdall.
However if you don't know your pattern this won't work!
Thanks!
Where can I download the "MEME" for local using?