blast against Repbase using Repeatmasker or blast

lran2008 · 08-15-2013, 01:00 PM

Hi all,

I would like to filter out the reads which matches with the repeats from miRNA seq data.

I am planing to use blastn to blast my data against the repeats fasta file from Repbase (http://www.girinst.org/censor/index.php). Will it work?

Because there is a RMBlast on RepeatMasker home page which is a RepeatMasker compatible version of the standard NCBI BLAST suite.
Here is the description for RMBlast:
The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler.
RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. These include:
• Support for custom matrices ( without KA-Statistics ).
• Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm.
• Support for cross_match-like masklevel filtering.

I just want to find the match between my short reads with the repeat database.So what is the difference?

SES · 08-16-2013, 07:52 AM

I would not worry about the differences for your purposes because it sounds like you are just interested in filtering reads. For that task, I think it's fine to just create a database and filter your reads based on matches. Make sure to turn off complexity filtering though.

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08-15-2013, 01:00 PM	#1
lran2008 Member Location: quebec Join Date: Apr 2013 Posts: 35	blast against Repbase using Repeatmasker or blast Hi all, I would like to filter out the reads which matches with the repeats from miRNA seq data. I am planing to use blastn to blast my data against the repeats fasta file from Repbase (http://www.girinst.org/censor/index.php). Will it work? Because there is a RMBlast on RepeatMasker home page which is a RepeatMasker compatible version of the standard NCBI BLAST suite. Here is the description for RMBlast: The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler. RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. These include: • Support for custom matrices ( without KA-Statistics ). • Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm. • Support for cross_match-like masklevel filtering. I just want to find the match between my short reads with the repeat database.So what is the difference?

08-16-2013, 07:52 AM	#2
SES Senior Member Location: Vancouver, BC Join Date: Mar 2010 Posts: 275	I would not worry about the differences for your purposes because it sounds like you are just interested in filtering reads. For that task, I think it's fine to just create a database and filter your reads based on matches. Make sure to turn off complexity filtering though.