The workflow sample, described below, allows one to do remote queries to the NCBI BLAST database to search for homologous nucleotide sequences for multiple input sequences at the same time.
As the result of the BLAST each input sequence is annotated with the "blast result" annotations. These annotations are used to fetch the corresponding homologous sequences from the NCBI database based on the identifiers specified in the "blast result" annotations. The output homologous sequences and the original sequences, annotated by BLAST, are grouped by folders.
Internet connection is required for running this workflow sample.
If you haven't used the workflow samples in UGENE before, look at the "How to Use Sample Workflows" section of the documentation.
The workflow sample "Remote BLASTing" can be found in the "Scenarios" section of the Workflow Designer samples.
The opened workflow looks as follows:
<center> <br> <img src="/wiki/download/attachments/16122736/Remote BLASTing.png"/> <br> </center>
The wizard has 3 pages.
Input Sequence(s) Page: On this page you must input at least one nucleotide sequence.
<center> <br> <img src="/wiki/download/attachments/16122736/Remote BLASTing_1.png"/> <br> </center>
For example, you can use the following two files as an input to the workflow:
Remote Nucleotide BLAST Page: Here you can optionally modify parameters that should be used for the remote BLAST queries. For example, you can select the search database, correct the e-value and set the maximum number of results (i.e. "Max hits"). The "Megablast" option, applied by default, specifies to optimize the search for high similar sequences only. Selecting it decreases the search time, but some less similar results could be skipped by the search in this case. Note that the "Megablast" option is also applied by default in the NCBI BLAST web interface.
<center> <br> <img src="/wiki/download/attachments/16122736/Remote BLASTing_2.png"/> <br> </center>
There are also some additional parameters. Description of them can be found in the Remote BLAST workflow element chapter of the documentation.
<center> <br> <img src="/wiki/download/attachments/16122736/Remote BLASTing_3.png"/> <br> </center>
The results on the hard drive are grouped by folders (see below).
The wizard page looks as follows:
<center> <br> <img src="/wiki/download/attachments/16122736/Remote BLASTing_4.png"/> <br> </center>
The workflow output files are shown in the dashboard as follows:
<center> <br> <img src="/wiki/download/attachments/16122736/Remote BLASTing_5.png"/> <br> </center>
Each file can be opened in the UGENE Sequence View by clicking on the corresponding link in the dashboard.
On the hard drive the output is grouped by folders with the names of the input sequences. For example, for the input sequences specified above, the output hierarchy will be the following: