Hello,

Here is a link to some documentation from a Tool Shed's version of the tool (don't worry to much about the particular repository or version, this is just a particularly nice document):
http://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=860f5cf73e01ebca&tool_config=database/community_files/000/repo_240/tools/ncbi_blast_plus/blastxml_to_tabular.xml&changeset_revision=45ba7c750bc8

"qframe" is the 'query frame' - this is not the same as coverage.

How to calculate coverage is up to you and may not be simple if you have overlapping HSPs. However, the basic concept is: total unique query bases included in any HSP/total query length is common. You will find with a quick web search that many people end up writing their own parser (directly from the alignment, not the tabular output) to get to this exact information, calculated in the way that they want it.

Best,

Jen
Galaxy team

On 2/3/14 11:20 AM, Deepak Datta wrote:

Hello,

I was working with NCBI BLAST + blastx.. I have a question regarding one of the columns that reads 'qframe'.

When we do Blast on NCBI, we get a column called query coverage. And when we perform NCBI BLAST + blastx, we get 25 columns. I wanted to know which of these columns is analogous to the "query coverage" column. And if these columns do not correspond to "query coverage" then can you kindly let me know how am I supposed to derive that?

Looking forward to your response.

--
DD
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