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Given this BLAST output, how can I determine the percentage of the query sequence in the alignment? I know that it's also referred to as 'query cover' but I can't seem to find anything online that tells me how to calculate this.

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I have given it a go and valued it as 145/147, but I'm not too sure on this. Can anybody clarify whether or not this is correct? Any help is highly appreciated

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  • $\begingroup$ Please don't post images of text. Instead, use the formatting tools and add the text directly into your question. That way, we can copy it and test our answers. Also, since this is essentially a scripting question, please clarify what operating system you are using so we know what type of answer to provide. I assume you realize that your output shows that residues 4 through 146 of a 146aa query are aligned, right? $\endgroup$ – terdon May 5 '15 at 12:05
  • $\begingroup$ qcovs and qcovshsp are reported.. In standalone BLAST you can specify the output format too $\endgroup$ – WYSIWYG May 5 '15 at 12:20
  • $\begingroup$ How can I do it without using BLAST? Just by looking at this output. $\endgroup$ – eyes enberg May 5 '15 at 12:23

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