Query cover in global alignment

Question

[el97004]

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.

[Carambakaracho]

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

[el97004]

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

[Carambakaracho]

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...

[el97004]

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

[el97004]

Thanks! I will give that a try.

Answer 1

[gb]

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.