Question: Is there any tool to convert blastx format from tabular to xml for feeding it to blast2go?
1
gravatar for seta
4.1 years ago by
seta1.2k
Sweden
seta1.2k wrote:

Dear all,

I'm busy with annotating transcriptome assembly by running blastx against some databases, I usually use outfmt 6 and it's not too much time-consuming, but as far as I know the blastx results have to feed to blast2go software in xml format. In my experience, doing blastx with xml output format is really time-consuming and painful. Could you please let me know if there is any tool to convert blastx output from tabular to xml? or there is any option or setting to accept tabular format of blastx results in the blast2go software? Thanks a lot for sharing your knowledge in this regard.

ADD COMMENTlink modified 17 days ago by Shahzad10 • written 4.1 years ago by seta1.2k

converting the tabular format to xml is like trying to make a cow from a steak.

ADD REPLYlink written 4.1 years ago by Pierre Lindenbaum122k

why don't you use annoncrypt for annotating the transcriptome ? It does pretty much you need.

ADD REPLYlink written 4.1 years ago by geek_y9.8k

Do you have the blast database locally? That could be an option. If you have local database and 8 CPUs on which to run you can blast a full transcriptome in a couple of days (nothing compared to the time it will take to blast2go!). 

 

ADD REPLYlink written 4.1 years ago by Fabio Marroni2.3k

Yeah, I did blastx locally with tabular output format while the acceptable output for blast2go is xml, doing blastx with xml output format takes too much time. so, I'm looking for a way to convert tabular output to xml format, that sounds that no way to do this. Could anybody please suggest experience to do blastx with xml output format at a reasonable time?

ADD REPLYlink written 4.1 years ago by seta1.2k
0
gravatar for Shahzad
17 days ago by
Shahzad10
Pakistan
Shahzad10 wrote:

please share if any body has solved this?

ADD COMMENTlink written 17 days ago by Shahzad10
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