blast against Repbase using Repeatmasker or blast

[lran2008]

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]

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.