Question: A Result From Mummer Alignment
3
gravatar for Love
8.5 years ago by
Love100
Love100 wrote:

Hello, I run the mummer command for a pairwaise alignment

mummer -s -mum refer.txt query.txt > refer_query.align

The result is:

> query
1450      9370        21

gaggttgcagtgagctgagat

2122      9771        21

caaaaaaaaaaaaaaaaaaaa

3296      9570        26

gaggtcaggagatcgagaccatcctg

3318      9243        20

cctgaccaacatggtgaaac

3428      9353        30

cttgaacctgggaggcagaggttgcagtga

3461      9386        20

gagatcatgccactgcactc

3502      9773        20

aaaaaaaaaaaaaaaaaaag

My question is the result seems only display the matched strings in the query sequence. Can we also show the ones in the reference sequence?

alignment • 6.3k views
ADD COMMENTlink written 8.5 years ago by Love100
1

If you are interested in variants, you can try dnadiff from MUMmer.

ADD REPLYlink written 8.5 years ago by lh332k
6
gravatar for Vitis
8.5 years ago by
Vitis2.3k
New York
Vitis2.3k wrote:

I wonder what kind of alignment view you want or you need any specific format to parse with perl or python. The usual way I do nucleotide alignment with mummer is following:

align the two sequences

nucmer -p out seq1.fa seq2.fa

filter the results (delta format)

delta-filter -g -u 95 out.delta > out.fil.delta

show the alingment records (matching string coordinates)

show-coords -c -l -r -T out.fil.delta > out.fil.coords

show alignments for the regions you want (something like clustalw results)

show-aligns -r .....

ADD COMMENTlink modified 8.5 years ago • written 8.5 years ago by Vitis2.3k

What I want to find at least say at least 80% identical match in reference and query. I need their positions in both sequence and letters. For example,

AGCTG 51 55 AGTTG 78 82

They have 4 same letters in 5. 4/5=80%

ADD REPLYlink written 8.5 years ago by Love100

I think you may need to filter based on identity at delta-filter part then use 'show-coords' to find the coordinates, then fetch the sequences from seq1 and seq2. There are a lot more stuff in the manual that I can't remember but I'm sure you'll find solutions there.

ADD REPLYlink written 8.5 years ago by Vitis2.3k

Yes, I found delta-filter. What is meant by the header.
such as:

tagA1 tagB1 500 20000000

ADD REPLYlink written 8.5 years ago by Love100

I might spoke it correctly. Do you mean I need to create a delta file first? My question is that because nucmer uses mummer for its maximal exact matching, can I also find non-match?Is it an align file? How to generate it?

ADD REPLYlink written 8.5 years ago by Love100

I might spoke it incorrectly. Do you mean I need to create a delta file first? My question is that because nucmer uses mummer for its maximal exact matching, can I also find non-match?Is it an align file? How to generate it?

ADD REPLYlink written 8.5 years ago by Love100

I used the command nucmer -p out seq1.fa seq2.fa to align the two sequences, but why the align file is empty?

ADD REPLYlink written 8.5 years ago by Love100

any error message? You should see a file named out.delta, it's empty?

ADD REPLYlink written 8.5 years ago by Vitis2.3k

The file exists but is empty(0kb). Do seq1.fa and seq2.fa need same length?

ADD REPLYlink written 8.5 years ago by Love100

that's quite strange, they don't have to be the same length. Are you sure they align with each other?

ADD REPLYlink written 8.5 years ago by Vitis2.3k

I upload files here. Could you help me to look at them?

ADD REPLYlink written 8.5 years ago by Love100

I uploaded files here. Could you please help me to look at them?

ADD REPLYlink modified 8 months ago by RamRS27k • written 8.5 years ago by Love100

simply run 'nucmer refer.txt query.txt' I got a 'out.delta' and the alignment information. I'm working on RedHat 64 bit with the most recent version of mummer. The output is like this:

NUCMER 91432805 20000 20000 3232 3487 9156 9412 44 44 0 33 -32 -1 -55 8 0

ADD REPLYlink written 8.5 years ago by Vitis2.3k

Any way to take this conversation to private emails? I may be able to help you troubleshoot the problem.

ADD REPLYlink written 8.5 years ago by Vitis2.3k

Yes, it is a good idea. How can I find your email from the profile?

ADD REPLYlink written 8.5 years ago by Love100
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