Question: Query Regarding Ncbi Blast+ Blastx
0
gravatar for Deepak Datta
4.6 years ago by
Deepak Datta10
Deepak Datta10 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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ADD COMMENTlink modified 4.6 years ago by Jennifer Hillman Jackson25k • written 4.6 years ago by Deepak Datta10
0
gravatar for Jennifer Hillman Jackson
4.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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=86 0f5cf73e01ebca&tool_config=database/community_files/000/repo_240/tools /ncbi_blast_plus/blastxml_to_tabular.xml&changeset_revision=45ba7c750b c8 "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 -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENTlink written 4.6 years ago by Jennifer Hillman Jackson25k
Hi Deepak, I suspect that the coverage number you are looking for is one of these values available with standalone BLAST+ tabular output: qcovs means Query Coverage Per Subject qcovhsp means Query Coverage Per HSP Neither of these are included in the standard 25 columns via Galaxy, but I'm hoping to add them later. See this discussion on the development list: http://dev.list.galaxyproject.org/Including-descriptions-etc-in- extended-BLAST-tabular-output-tc4662704.html It is encouraging to know people would use some of these 'extra' fields :) Peter
ADD REPLYlink written 4.6 years ago by Peter Cock1.4k
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