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Old 08-15-2013, 01:00 PM   #1
Location: quebec

Join Date: Apr 2013
Posts: 35
Default 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 ( 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?
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Old 08-16-2013, 07:52 AM   #2
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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.
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