Hi Heather,
Can you please give some examples of your motifs?
Also showing us the code that you use with cosmo can be useful.
Even if the matchPattern() function in Biostrings doesn't let you
control the number
of gaps, there might be workarounds, it all depends what your motifs
really look
like. And we need use cases anyway so we know where to put our
efforts. Thanks!
H.
Houseman, Heather wrote:
> Dear Bioconductor mailing list:
>
> I've been using cosmo to look for motifs. I'd like to search for
motifs that have a variable length of gaps in the middle. If I specify
a range of motif widths with the cosmo function, it uses the width
with the lowest BIC value and searches for motifs of only that width.
My dilemma is that the motifs I'm looking for are of variable width.
>
> Thanks in advance for any help!
>
> Heather
>
> This email message, including any attachments, is for
...{{dropped:8}}
Herve,
My ultimate goal is to find motifs in different sequences that are
similar to the ones below.
TACGTGCTGTCTCACACAG
GACGTGACTCGGACCACAT
TACGTGGGT--TTCCACAG
TACGTGAC----CACACAC
TACGTGC-------CACAG
CACGTGC-------CACAC
GGCGTGAGC-----CACCG
GGCGTGGGAGCG--CACAG
TACGTG------CACACAG
To start off, I'm inserting the motifs above into random sequences to
see if I can get cosmo to return those motifs. Once I get that
procedure to work, I'd like to use it to apply it to "real" sequences
and hopefully return motifs that look similar to the ones above.
Here's the cosmo code I'm using:
res = cosmo(seqs = seqs, minW = 12, maxW = 20, models = "OOPS")
Is this more along the lines of multiple sequence alignment and not
something that I can use cosmo for?
Thanks!
Heather
-----Original Message-----
From: Herve Pages [mailto:hpages@fhcrc.org]
Sent: Thursday, November 01, 2007 1:33 PM
To: Houseman, Heather
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] motif searching with variable length gaps
Hi Heather,
Can you please give some examples of your motifs?
Also showing us the code that you use with cosmo can be useful.
Even if the matchPattern() function in Biostrings doesn't let you
control the number
of gaps, there might be workarounds, it all depends what your motifs
really look
like. And we need use cases anyway so we know where to put our
efforts. Thanks!
H.
Houseman, Heather wrote:
> Dear Bioconductor mailing list:
>
> I've been using cosmo to look for motifs. I'd like to search for
motifs that have a variable length of gaps in the middle. If I specify
a range of motif widths with the cosmo function, it uses the width
with the lowest BIC value and searches for motifs of only that width.
My dilemma is that the motifs I'm looking for are of variable width.
>
> Thanks in advance for any help!
>
> Heather
>
> This email message, including any attachments, is for
...{{dropped:16}}
Hi Heather,
cosmo could find motifs like these as long as the total length of the
motif (2 outer parts + gap) is the same in each motif. If that's true,
your code should work.
Oliver
On Nov 1, 2007 11:10 AM, Houseman, Heather <heather.houseman at="" vai.org=""> wrote:
> Herve,
>
> My ultimate goal is to find motifs in different sequences that are
similar to the ones below.
>
> TACGTGCTGTCTCACACAG
> GACGTGACTCGGACCACAT
> TACGTGGGT--TTCCACAG
> TACGTGAC----CACACAC
> TACGTGC-------CACAG
> CACGTGC-------CACAC
> GGCGTGAGC-----CACCG
> GGCGTGGGAGCG--CACAG
> TACGTG------CACACAG
>
> To start off, I'm inserting the motifs above into random sequences
to see if I can get cosmo to return those motifs. Once I get that
procedure to work, I'd like to use it to apply it to "real" sequences
and hopefully return motifs that look similar to the ones above.
>
> Here's the cosmo code I'm using:
>
> res = cosmo(seqs = seqs, minW = 12, maxW = 20, models = "OOPS")
>
> Is this more along the lines of multiple sequence alignment and not
something that I can use cosmo for?
>
> Thanks!
>
> Heather
>
> -----Original Message-----
> From: Herve Pages [mailto:hpages at fhcrc.org]
> Sent: Thursday, November 01, 2007 1:33 PM
> To: Houseman, Heather
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] motif searching with variable length gaps
>
> Hi Heather,
>
> Can you please give some examples of your motifs?
>
> Also showing us the code that you use with cosmo can be useful.
>
> Even if the matchPattern() function in Biostrings doesn't let you
control the number
> of gaps, there might be workarounds, it all depends what your motifs
really look
> like. And we need use cases anyway so we know where to put our
efforts. Thanks!
>
> H.
>
>
> Houseman, Heather wrote:
> > Dear Bioconductor mailing list:
> >
> > I've been using cosmo to look for motifs. I'd like to search for
motifs that have a variable length of gaps in the middle. If I specify
a range of motif widths with the cosmo function, it uses the width
with the lowest BIC value and searches for motifs of only that width.
My dilemma is that the motifs I'm looking for are of variable width.
> >
> > Thanks in advance for any help!
> >
> > Heather
> >
> > This email message, including any attachments, is for
...{{dropped:16}}
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
Hi Heather,
Would this function work for you?
matchLRPatterns <- function(Lpattern, Rpattern, maxngaps, subject,
Lmismatch=0, Rmismatch=0)
{
Lmatches <- matchPattern(Lpattern, subject, mismatch=Lmismatch)
Rmatches <- matchPattern(Rpattern, subject, mismatch=Rmismatch)
ans_start <- ans_end <- integer(0)
for (i in seq_len(length(Lmatches))) {
ngaps <- start(Rmatches) - end(Lmatches)[i] - 1
jj <- which(0 <= ngaps & ngaps <= maxngaps)
ans_start <- c(ans_start, rep(start(Lmatches)[i], length(jj)))
ans_end <- c(ans_end, end(Rmatches)[jj])
}
views(subject, ans_start, ans_end)
}
Arguments:
o Lpattern, Rpattern: the left and right parts of your motif (for
example
TACGTGGGT and TTCCACAG for the 3rd motif you gave us: TACGTGGGT
--TTCCACAG)
o maxngaps: the max number of gaps in the middle i.e the distance
between
the left and right parts of your motif
o subject: a BString (or derived) object containing the subject
string
(in your case it needs to be a DNAString object)
o Lmismatch, Rmismatch: additionally you can choose to allow a given
number of
mismatches for the left and right parts of the motif
So for example if I want to search motif TACGTGGGT--TTCCACAG in
chromosome 1
of the mouse:
> library(BSgenome.Mmusculus.UCSC.mm9)
> chr1 <- Mmusculus$chr1
> matchLRPatterns("TACGTGGGT", "TTCCACAG", maxngaps=2, chr1)
Views on a 197195432-letter DNAString subject
Subject:
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...AAGAATTTGGTATTAAACTTAAAACTGGAATTC
Views: NONE
I don't find any match. But if I allow the number of gaps to be <= 150
instead of 2:
> matchLRPatterns("TACGTGGGT", "TTCCACAG", maxngaps=150, chr1)
Views on a 197195432-letter DNAString subject
Subject:
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...AAGAATTTGGTATTAAACTTAAAACTGGAATTC
Views:
start end width
[1] 193252084 193252245 162
[TACGTGGGTTCCTGACGATGGT...ATGTGAACTCTTTCTTCCACAG]
then I find one match.
Note that matchLRPatterns() will return all matches, even overlapping
matches:
> library(Biostrings)
> subject <- DNAString("AAATTAACCCTT")
> matchLRPatterns("AA", "TT", 0, subject)
Views on a 12-letter DNAString subject
Subject: AAATTAACCCTT
Views:
start end width
[1] 2 5 4 [AATT]
> matchLRPatterns("AA", "TT", 1, subject)
Views on a 12-letter DNAString subject
Subject: AAATTAACCCTT
Views:
start end width
[1] 1 5 5 [AAATT]
[2] 2 5 4 [AATT]
> matchLRPatterns("AA", "TT", 3, subject)
Views on a 12-letter DNAString subject
Subject: AAATTAACCCTT
Views:
start end width
[1] 1 5 5 [AAATT]
[2] 2 5 4 [AATT]
[3] 6 12 7 [AACCCTT]
> matchLRPatterns("AA", "TT", 7, subject)
Views on a 12-letter DNAString subject
Subject: AAATTAACCCTT
Views:
start end width
[1] 1 5 5 [AAATT]
[2] 2 5 4 [AATT]
[3] 2 12 11 [AATTAACCCTT]
[4] 6 12 7 [AACCCTT]
Also not that matches will always been ordered from left to right.
Please let me know if this is not what you want.
Cheers,
H.
Houseman, Heather wrote:
> Herve,
>
> My ultimate goal is to find motifs in different sequences that are
similar to the ones below.
>
> TACGTGCTGTCTCACACAG
> GACGTGACTCGGACCACAT
> TACGTGGGT--TTCCACAG
> TACGTGAC----CACACAC
> TACGTGC-------CACAG
> CACGTGC-------CACAC
> GGCGTGAGC-----CACCG
> GGCGTGGGAGCG--CACAG
> TACGTG------CACACAG
>
> To start off, I'm inserting the motifs above into random sequences
to see if I can get cosmo to return those motifs. Once I get that
procedure to work, I'd like to use it to apply it to "real" sequences
and hopefully return motifs that look similar to the ones above.
>
> Here's the cosmo code I'm using:
>
> res = cosmo(seqs = seqs, minW = 12, maxW = 20, models = "OOPS")
>
> Is this more along the lines of multiple sequence alignment and not
something that I can use cosmo for?
>
> Thanks!
>
> Heather
>
> -----Original Message-----
> From: Herve Pages [mailto:hpages at fhcrc.org]
> Sent: Thursday, November 01, 2007 1:33 PM
> To: Houseman, Heather
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] motif searching with variable length gaps
>
> Hi Heather,
>
> Can you please give some examples of your motifs?
>
> Also showing us the code that you use with cosmo can be useful.
>
> Even if the matchPattern() function in Biostrings doesn't let you
control the number
> of gaps, there might be workarounds, it all depends what your motifs
really look
> like. And we need use cases anyway so we know where to put our
efforts. Thanks!
>
> H.
>
>
> Houseman, Heather wrote:
>> Dear Bioconductor mailing list:
>>
>> I've been using cosmo to look for motifs. I'd like to search for
motifs that have a variable length of gaps in the middle. If I specify
a range of motif widths with the cosmo function, it uses the width
with the lowest BIC value and searches for motifs of only that width.
My dilemma is that the motifs I'm looking for are of variable width.
>>
>> Thanks in advance for any help!
>>
>> Heather
>>
>> This email message, including any attachments, is for
th...{{dropped:9}}
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> This email message, including any attachments, is for
...{{dropped:2}}
Hi Heather,
Unfortunately, the cosmo package doesn't have a functionality for this
kind of a search. It is always assumed that the shared motif is of the
same length.
Oliver
On Nov 1, 2007 8:40 AM, Houseman, Heather <heather.houseman at="" vai.org=""> wrote:
> Dear Bioconductor mailing list:
>
> I've been using cosmo to look for motifs. I'd like to search for
motifs that have a variable length of gaps in the middle. If I specify
a range of motif widths with the cosmo function, it uses the width
with the lowest BIC value and searches for motifs of only that width.
My dilemma is that the motifs I'm looking for are of variable width.
>
> Thanks in advance for any help!
>
> Heather
>
> This email message, including any attachments, is for
...{{dropped:9}}
Hi Heather,
If your goal at this point is to insert motifs like the ones above
into random sequences to see if cosmo can find them, you should be
able to use any character you like for the gaps. Since a gap in a
motif just says that the specific nucleotide is not important, you
could in particular just fill in random A, C, G, T letters. If you
don't want to do that, something like "X" or "N" should also work. It
sounds like you already got it to work with the "N".
I hope this helps.
Oliver
On Nov 1, 2007 11:38 AM, Houseman, Heather <heather.houseman at="" vai.org=""> wrote:
> Hello Oliver,
>
> What symbol should I use for gaps? I tried a "-" for each gap, but
cosmo returned an error. I then tried a "0" for each gap and cosmo
didn't return an error, but the motifs it returned didn't contain any
0's, so I assumed it didn't "like" them. I tried an "N" for each gap
and it didn't return an error and the motifs contained N's. I realize
that an "N" is not the same as a gap. I was just seeing if it would
work.
>
> What strategy do you suggest? Should I use some other function to
align the sequences, which would most likely put gaps in them, and
then use those sequences with gaps with cosmo to return motifs? But
then, I'm back to the question of what symbol to use for the gaps.
>
> Thanks for your help!
>
> Heather
>
> -----Original Message-----
> From: Oliver Bembom [mailto:oliver.bembom at gmail.com]
> Sent: Thursday, November 01, 2007 2:24 PM
> To: Houseman, Heather
>
> Cc: Herve Pages; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] motif searching with variable length gaps
>
> Hi Heather,
>
> cosmo could find motifs like these as long as the total length of
the
> motif (2 outer parts + gap) is the same in each motif. If that's
true,
> your code should work.
>
> Oliver
>
> On Nov 1, 2007 11:10 AM, Houseman, Heather <heather.houseman at="" vai.org=""> wrote:
> > Herve,
> >
> > My ultimate goal is to find motifs in different sequences that are
similar to the ones below.
> >
> > TACGTGCTGTCTCACACAG
> > GACGTGACTCGGACCACAT
> > TACGTGGGT--TTCCACAG
> > TACGTGAC----CACACAC
> > TACGTGC-------CACAG
> > CACGTGC-------CACAC
> > GGCGTGAGC-----CACCG
> > GGCGTGGGAGCG--CACAG
> > TACGTG------CACACAG
> >
> > To start off, I'm inserting the motifs above into random sequences
to see if I can get cosmo to return those motifs. Once I get that
procedure to work, I'd like to use it to apply it to "real" sequences
and hopefully return motifs that look similar to the ones above.
> >
> > Here's the cosmo code I'm using:
> >
> > res = cosmo(seqs = seqs, minW = 12, maxW = 20, models = "OOPS")
> >
> > Is this more along the lines of multiple sequence alignment and
not something that I can use cosmo for?
> >
> > Thanks!
> >
> > Heather
> >
> > -----Original Message-----
> > From: Herve Pages [mailto:hpages at fhcrc.org]
> > Sent: Thursday, November 01, 2007 1:33 PM
> > To: Houseman, Heather
> > Cc: bioconductor at stat.math.ethz.ch
> > Subject: Re: [BioC] motif searching with variable length gaps
> >
> > Hi Heather,
> >
> > Can you please give some examples of your motifs?
> >
> > Also showing us the code that you use with cosmo can be useful.
> >
> > Even if the matchPattern() function in Biostrings doesn't let you
control the number
> > of gaps, there might be workarounds, it all depends what your
motifs really look
> > like. And we need use cases anyway so we know where to put our
efforts. Thanks!
> >
> > H.
> >
> >
> > Houseman, Heather wrote:
> > > Dear Bioconductor mailing list:
> > >
> > > I've been using cosmo to look for motifs. I'd like to search
for motifs that have a variable length of gaps in the middle. If I
specify a range of motif widths with the cosmo function, it uses the
width with the lowest BIC value and searches for motifs of only that
width. My dilemma is that the motifs I'm looking for are of variable
width.
> > >
> > > Thanks in advance for any help!
> > >
> > > Heather
> > >
> > > This email message, including any attachments, is for
...{{dropped:16}}
> >
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> This email message, including any attachments, is for
...{{dropped:3}}
