Question: Mummer To Viewable Alignment Format (Fasta Or Aln...)
2
gravatar for Yannick Wurm
9.4 years ago by
Yannick Wurm2.3k
Queen Mary University London
Yannick Wurm2.3k wrote:

Hi,

I'm aligning pairs of genomic scaffolds, looking for 1000bp-size insertions/deletions. Its easy to get a dotplot for an overview. It's also easy to find SNPs at a small-scale. But I need to find putative insertions and subsequently confirm them in the lab. Thus I need something I can open in Jalview or something else, where it is easy to see the insertions and to copy-paste the relevant sequences into something for primer design.

I can get such alignments in useable time with clustal (sorry), but not if both sequences are 1MB or bigger. Mummer is super fast, but has a weird output format. Anything else I could use that is fast but gives a user-friendly output? (BLAST would be great, but it divides the aligning bits up into multiple HSPs instead of one long contiguous alignment).

Cheers yannick

alignment genomics • 5.5k views
ADD COMMENTlink written 9.4 years ago by Yannick Wurm2.3k
1

Would the 'show-aligns' command in Mummer package help? I used that for relative small regions. Btw, from the Mummer output (like 'show-snps') you can get snp/indel positions with flanking regions. I used that for grabbing sequences and pipe into primer3 to get primers.

ADD REPLYlink written 9.4 years ago by Vitis2.4k

Hi Vitis & thanks for the suggestion. Yes, for small inserts it works ... but I'm interested in multiple-kb insertions. Those are split into different "aligns" by mummer...

ADD REPLYlink written 9.4 years ago by Yannick Wurm2.3k
4
gravatar for ALchEmiXt
9.4 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

You can parse the 'coords' file of MUMmer (which you can get using the --coords option) into a so-called BLAST-crunch file. That file can directly be read into for instance Artemis Comparsion Tool (ACT of Sanger see their website).

An example on the galaxy platform we have posted a while ago. here where you can just grab the perl nucmer_coords2ACT_galaxy.pl file.

Basically all it does is to calculate a score. For example:

while (<COORDS>)
    {
    unless ($_ =~ /^(\s*)\d/){next}
    $_ =~ s/\|//g;

    my @f = split;
          # create crude match score = ((length_of_match * %identity)-(length_of_match * (100 - %identity))) /20
    my $crude_plus_score=($f[4]*$f[6]);
    my $crude_minus_score=($f[4]*(100-$f[6]));
    my $crude_score=  int(($crude_plus_score  - $crude_minus_score) / 20);
          # reorganise columns and print crunch format to stdout
          # score        %id   S1    E1    seq1  S2    E2    seq2  (description)
    print OUT " $crude_score $f[6] $f[0] $f[1] $f[7] $f[2] $f[3] $f[8] nucmer comparison coordinates\n"
    }
ADD COMMENTlink written 9.4 years ago by ALchEmiXt1.9k

thanks for the quick reply. can you copy-paste nucleotides out from ACT?

ADD REPLYlink written 9.4 years ago by Yannick Wurm2.3k

yes. The ACT and Artemis suites are meant for annotation/curation onto the single nt level: http://www.sanger.ac.uk/resources/software/artemis/ There is Artemis for single sequence and ArtemisComparisonTool (ACT) for multiple sequences.

ADD REPLYlink written 9.4 years ago by ALchEmiXt1.9k
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