converting between different blast output and their visualizations

Question: converting between different blast output and their visualizations

7 months ago by

ruchi.jain • 0

United States

ruchi.jain • 0 wrote:

Hi,

I ran a tblastX for a fasta dataset (paired sequences) against a fasta file (gene of interest). I have few questions:

I made the db from the fast file but it doesn't show up when i do tblastx. Why?
I have the output in extended tabular form, can I easily change it to the multiple seq alignment form or should I rerun the whole analysis?
What is the best way to get information about of this heavy tabular file? I am unable to even import in excel as it is too big.

Please suggest

Thanks Ruchi

graph manipulation blast+ statistics tabular • 271 views

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modified 7 months ago • written 7 months ago by ruchi.jain • 0

7 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Replies per question:

It looks like you have solved this problem. I see a successful database creation (nucleotide) and two successful tBlastx jobs (using that database along with a nucleotide query).
Use one of the output options labeled "Query-anchored". Quote from the tool form:

The two query anchored outputs show a multiple sequence alignment between the query and all the matches, and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).

Tabular data manipulation: Common tools are in the groups: Text Manipulation; Datamash; Convert Formats; Filter and Sort; Join, Subtract and Group. Tabular data (original output or filtered/manipulated output that is still in tabular format) can be graphed using the Charts/Scatterplot functions (click on the small graph icon within a dataset to access these) or with tools in the groups Graph/Display Data and Statistics.

Galaxy tutorials, try the 101 first for an overview of some of the data manipulation functions: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson ♦ 25k

7 months ago by

ruchi.jain • 0

United States

ruchi.jain • 0 wrote:

Thanks Jen for your reply!

I have a nucleotide database and wants to align the sequences to be aligned to my query but after translation. I am trying to see SNPs that result in amino acid changes. I checked ClustalW as per your suggestion but its for the same query and subject type. Do you have any suggestion for that ?

Thanks

ADD COMMENT • link written 7 months ago by ruchi.jain • 0

Try the "Query-anchored" output option. I updated the reply shortly after posting. You won't need to use ClustalW, instead, you can use tBlastx directly.

ADD REPLY • link written 7 months ago by Jennifer Hillman Jackson ♦ 25k

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