DNA multiple sequence alignment with strand direction
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James
Dec 15, 2011, 10:44:58 AM12/15/11
to Tcoffee
dear all,
Is there a way to do DNA multiple sequence alignments with tcoffee
such that it will optimise relative strand orientations as well (i.e.
flip individual sequences to inverse complement if this produces a
better overall MSA)?
Obviously one can do this manually by doing MSA of all possible
combinations of strand orientations but it would be nice to do this in
one step.
best wishes,
James.
Genevieve Thompson
Apr 3, 2013, 5:30:51 AM4/3/13
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Hi James,
Any chance you figured out a way to do this? I need to work through around 3000 sequences that were all downloaded from GenBank so an automated approach to testing both directions of the same sequence, would be ideal.
Many thanks,
Gen
Any chance you figured out a way to do this? I need to work through around 3000 sequences that were all downloaded from GenBank so an automated approach to testing both directions of the same sequence, would be ideal.
Many thanks,
Gen
James MacDonald
Apr 5, 2013, 7:10:05 AM4/5/13
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Hi Gen,
I didn't get any reply to this. I think in general people writing sequence alignment software concentrate on protein sequences as it is easier and clearer what to optimise for.
I guess the thing with this specific problem is the combinatorial explosion if you have too many sequences. There are motif searching software which produce gapped multiple alignments such as glam2 which you might want to use but they take a while to run. I ended up using glam2 myself.
best wishes,
James.
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cnotredame
Apr 5, 2013, 8:21:35 AM4/5/13
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Hi Gen,
IF I understand, you would like to dump the sequence and let the aligner
decide if a given sequence has to be taken 5'->3' or reversed to fit in
the MSA. Is this correct?
T-Coffee cannot do this for you assumes you already have the sequences
in the right orientation.
I do not know any piece of code doing this for you. As James points out,
the full pb is very heay. It's like if you had to consider all the
possible sets with sequences flipped or unfilpped, which means 2^3000
combinations to try in yet case.
Yet, it can be very simply solved in a progressive. Most aligners group
the sequences along a tree and then floow the tree aligning either pairs
of sequences or pairs of profile at each node. T-Coffee, muscle,
clustal, everything works more or less this way. When collapsing a note,
it would be totally trivila to test which pairwise alignment gives the
best score. That would only double computation time. Any regular aligner
(including T-Coffee) could easily be hacked to do this. I will if I have
a bit of time.
Is it a problem you often have?
Cheers,
Cedric
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IF I understand, you would like to dump the sequence and let the aligner
decide if a given sequence has to be taken 5'->3' or reversed to fit in
the MSA. Is this correct?
T-Coffee cannot do this for you assumes you already have the sequences
in the right orientation.
I do not know any piece of code doing this for you. As James points out,
the full pb is very heay. It's like if you had to consider all the
possible sets with sequences flipped or unfilpped, which means 2^3000
combinations to try in yet case.
Yet, it can be very simply solved in a progressive. Most aligners group
the sequences along a tree and then floow the tree aligning either pairs
of sequences or pairs of profile at each node. T-Coffee, muscle,
clustal, everything works more or less this way. When collapsing a note,
it would be totally trivila to test which pairwise alignment gives the
best score. That would only double computation time. Any regular aligner
(including T-Coffee) could easily be hacked to do this. I will if I have
a bit of time.
Is it a problem you often have?
Cheers,
Cedric
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!New TEDex Talk:http://www.youtube.com/watch?v=cFcHGuMNKwA
Dr Cedric Notredame
Group Leader
Notredame's lab - Comparative Bioinformatics Group
Bioinformatics and Genomics Programme
Room 440.03
Centre de Regulacio Genomica (CRG)
Dr. Aiguader, 88
08003 Barcelona
Spain
Ph# + 34 93 316 02 71
Fax# + 34 93 316 00 99
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###########################################
Genevieve Thompson
Apr 9, 2013, 10:57:59 AM4/9/13
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Hi James and Cedric,
Thanks for your responses and suggestions! I will have a look at glam2....
Since my post I came up with a potential solution in R that I am writing code for at the moment. It uses a reference sequence (sequence of known orientation and of high quality) to conduct a pairwise alignment between the reference sequence and every other non reference sequence in my dataset. This is linked to MUMSA and should produce a table of results listing the sequence tested, and its overlap score. I am hoping this will allow me to get rid of the junk, and ID sequences that need to be individually checked and edited etc.... hopefully it will work! I have been searching for alternate options and (very) recently came across another piece of software (MIRA) that is actually used for alignment in next gen projects, and appears to be pretty comprehensive in function - I am still figuring out if the software can be used for what I need though - the manual is 200 pages :/
To answer your question Cedric, I will only need this function for the current project so a large investment of your time may not be the way forward right now, although I very much appreciate the offer. However, off-hand, I can think of a large number of ecologists that would find such a function very useful as phylogenetic information is increasingly being incorporated into field ecology. I know that I would personally use it for future research, so when you have some time....Thanks for your responses and suggestions! I will have a look at glam2....
Since my post I came up with a potential solution in R that I am writing code for at the moment. It uses a reference sequence (sequence of known orientation and of high quality) to conduct a pairwise alignment between the reference sequence and every other non reference sequence in my dataset. This is linked to MUMSA and should produce a table of results listing the sequence tested, and its overlap score. I am hoping this will allow me to get rid of the junk, and ID sequences that need to be individually checked and edited etc.... hopefully it will work! I have been searching for alternate options and (very) recently came across another piece of software (MIRA) that is actually used for alignment in next gen projects, and appears to be pretty comprehensive in function - I am still figuring out if the software can be used for what I need though - the manual is 200 pages :/
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Cedric Notredame
Apr 9, 2013, 6:59:53 PM4/9/13
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Hi Gen,
Your R solution could work provided your sequences are close enough so
that you can distinguish the sense/antisense. Indeed you have a choice
to either align everything to your chosen sequence, but you may loose
the outliers, or grow a profile one sequence at a time, which can be
computationally inefficient with large datasets (because the frofile
length tends to grow which means much more computation than when doing a
tree based alignment)
Cheers,
Cedric
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Your R solution could work provided your sequences are close enough so
that you can distinguish the sense/antisense. Indeed you have a choice
to either align everything to your chosen sequence, but you may loose
the outliers, or grow a profile one sequence at a time, which can be
computationally inefficient with large datasets (because the frofile
length tends to grow which means much more computation than when doing a
tree based alignment)
Cheers,
Cedric
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Genevieve Thompson
Apr 10, 2013, 3:08:34 AM4/10/13
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Hi Cedric,
Thanks - yes I should have mentioned that I will be using two reference sequences per family/major clade (info taken from an old matk tree) to create a bunch of sub-alignments. The final step would be to use T coffee to align these subalignments into a single alignment. I am hoping this will be possible with T coffee?
Thanks again for your help!Thanks - yes I should have mentioned that I will be using two reference sequences per family/major clade (info taken from an old matk tree) to create a bunch of sub-alignments. The final step would be to use T coffee to align these subalignments into a single alignment. I am hoping this will be possible with T coffee?
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Room 440.03
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Cedric Notredame
Apr 10, 2013, 8:46:14 AM4/10/13
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yes, you should be able to use the profile option: t_coffee -profile
<msa1>, <msa2>
BTW, if your sequences are close enough, a simple trick could be to run
a fast clustering algo, like uclust, blastclust, or anything you like,
multiply align sequences in each cluster, and then align your two
clusters, whilst testing the orientation of one of the clusters.
If you are lucky and your sequences are close enough, you will only get
two clusters, 5' 3' and the reverse.
To test the two direction, you can use seq_reformat (part of T-Coffee)
with the option:
t_coffee -other_pg seq_reformat -in <fasta or msa> -acion +complement
Cheers,
Cedric
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<msa1>, <msa2>
BTW, if your sequences are close enough, a simple trick could be to run
a fast clustering algo, like uclust, blastclust, or anything you like,
multiply align sequences in each cluster, and then align your two
clusters, whilst testing the orientation of one of the clusters.
If you are lucky and your sequences are close enough, you will only get
two clusters, 5' 3' and the reverse.
To test the two direction, you can use seq_reformat (part of T-Coffee)
with the option:
t_coffee -other_pg seq_reformat -in <fasta or msa> -acion +complement
Cheers,
Cedric
> <mailto:j.macdonald@imperial.__ac.uk
> <mailto:j.mac...@imperial.ac.uk>>> wrote:
>
> Hi Gen,
>
> I didn't get any reply to this. I think in general people
> writing
> sequence alignment software concentrate on protein
> sequences as it
> is easier and clearer what to optimise for.
>
> I guess the thing with this specific problem is the
> combinatorial
> explosion if you have too many sequences. There are motif
> searching
> software which produce gapped multiple alignments such as glam2
> which you might want to use but they take a while to run. I
> ended up
> using glam2 myself.
>
> best wishes,
> James.
>
> On Wed, Apr 3, 2013 at 10:30 AM, Genevieve Thompson
> <geneviev...@gmail.com <mailto:geneviev...@gmail.com>
>
> Hi Gen,
>
> I didn't get any reply to this. I think in general people
> writing
> sequence alignment software concentrate on protein
> sequences as it
> is easier and clearer what to optimise for.
>
> I guess the thing with this specific problem is the
> combinatorial
> explosion if you have too many sequences. There are motif
> searching
> software which produce gapped multiple alignments such as glam2
> which you might want to use but they take a while to run. I
> ended up
> using glam2 myself.
>
> best wishes,
> James.
>
> On Wed, Apr 3, 2013 at 10:30 AM, Genevieve Thompson
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> Bioinformatics and Genomics Programme
> Room 440.03
>
> Centre de Regulacio Genomica (CRG)
> Dr. Aiguader, 88
> 08003 Barcelona
> Spain
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Genevieve Thompson
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The BTW is very useful!! :)
I will definitely take your advice and make use of the provided commands. Thanks!<mailto:j.macdonald@imperial.__ac.uk
<mailto:j.macdonald@imperial.ac.uk>>> wrote:
Hi Gen,
I didn't get any reply to this. I think in general people
writing
sequence alignment software concentrate on protein
sequences as it
is easier and clearer what to optimise for.
I guess the thing with this specific problem is the
combinatorial
explosion if you have too many sequences. There are motif
searching
software which produce gapped multiple alignments such as glam2
which you might want to use but they take a while to run. I
ended up
using glam2 myself.
best wishes,
James.
On Wed, Apr 3, 2013 at 10:30 AM, Genevieve Thompson
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