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*
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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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-BLA... It is encouraging to know people would use some of these 'extra' fields :) Peter On Tue, Feb 4, 2014 at 3:59 PM, Jennifer Jackson <jen@bx.psu.edu> 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=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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
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-- Jennifer Hillman-Jackson http://galaxyproject.org
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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participants (3)
-
Deepak Datta -
Jennifer Jackson -
Peter Cock