Question: Query cover in global alignment
1
gravatar for el97004
14 days ago by
el9700410
el9700410 wrote:

Hi,

Does anyone know how I can modify the command line parameters in needleall to output query coverage? So far my code below only gives me values for Identity, similarity, gaps, and score.

needleall -asequence proteins_f1.fa -bsequence proteins_f2.fa -outfile needle_results -aformat pair -gapopen 10 -gapextend 0.5

Thanks very much.

ADD COMMENTlink modified 12 days ago by gb1.0k • written 14 days ago by el9700410

Dear el97004, you compare two protein sequences using an alignment algorithm. There's a few misconceptions in you're question

  1. Coverage usually describes sequencing depth of DNA sequencing
  2. Sequence alignments yield similarity scores (like you get), not coverage
ADD REPLYlink written 14 days ago by Carambakaracho1.8k

Hi Carambakaracho , I am referring to query coverage in sequence alignments not sequencing depth. From Blast documentation: The query cover is a number that describes how much of the query sequence is covered by the target sequence. This tells us how long the sequences are, relative to each other

ADD REPLYlink modified 14 days ago • written 14 days ago by el9700410
1

uhoh, my bad...

To recompense for my poorly qualified comment let me direct you to the help page of needleall. I believe their layout was bad already when the internet was born, and it's only topped by the obscure commandline switches. My best guess is the -awidth3 switch does what you want. But with these EMBOSS tools, I have a lot of experience with trial and error and not getting where I wanted...

ADD REPLYlink modified 14 days ago • written 14 days ago by Carambakaracho1.8k

Thanks! I will give that a try.

ADD REPLYlink written 13 days ago by el9700410

Unfortunately -awidth3 does not do it. However as I am thinking more about this problem, perhaps query coverage does not really make sense for global alignments since they are trying to align proteins from end to end, so i think % query cover in a global alignment may just be the same as the % identity value

ADD REPLYlink modified 13 days ago • written 13 days ago by el9700410
2
gravatar for gb
12 days ago by
gb1.0k
gb1.0k wrote:

A global alignment does not give a coverage. "It will always try a coverage of 100%", a global alignment will try to align the full sequence in the best possible way.

ADD COMMENTlink written 12 days ago by gb1.0k
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