[Gramene] Help regarding BLAST result summary

[William Spooner]

>> From: "Mauro-Herrera, Margarita" <margarita.mauro- 
>> herrera at okstate.edu>
>> Date: November 3, 2008 11:19:13 AM CST
>> To: "gramene at gramene.org" <gramene at gramene.org>
>> Subject: [Gramene] Help regarding BLAST result summary
>>
>> Hello,
>>  My name is Margarita Mauro and I have been doing some BLAST  
>> searches using Gramene. It is working fine with the exception that  
>> there is a step that is taking a loong time when I do my alignments  
>> with the sequences/hits from my BLAST searches. That is putting all  
>> the hits/sequences in the same orientation so I can do my  
>> alignments with MAFFT (the alignment program that requires all the  
>> sequences to be in the same orientation). I wonder if there is a  
>> way to get the orientation of the sequences/hits as another column  
>> in the BLAST result summary table (where you get the hit ID, the  
>> BLAST score and the BLAST E-value)? Or if the information regarding  
>> the direction of the hit sequences with respect to the query can be  
>> downloaded somehow when you display the hits as FASTA files?
>>
>> Please, let me know if you understand my questions and if there is  
>> anything that can be done to help me out.
>> Thanks in advance and I look forward to hearing from you,
>> Margarita

Hi Margarita,

I'm looking at the results table now for an example search; a rice EST  
blastn against the rice genome sequence, and I can see both query  
orientation and chromosome orientation fields displayed. These fields  
can be toggled on/off by the user, so they may potentially be turned  
off in your case.

Does this help, or do you still have a problem seeing these fields, or  
I may not be understanding you correctly.

All the best,

Will