Question RepeatMasker vs. BLAST - e-Value

[voidnyx]

Hi,

So I was looking at my data with RepeatMasker for some repetitive ~100bp sequences from my customRepLib. I was just looking for their distribution and positions so not exactly masking them and I used the rm-blast search engine that is a modified version of BLAST to work with RM.

Now I have some (non-repetivie) sequence that maybe assoziated to the repetitive elements and I searched for that one too with RepeatMasker since RM generates a convenient HTML output of its findings and I could just use 1 programm for all the searching.


The drawback is, RM offers no e-values for its alignments just a Smith-Waterman Score. When I searched for a way to calculate the e-value myself I got doubts if I am using the right tool here and the more I thought abtout it the insecurer I got.


So the question is twofold:

1. Is it actually a viable way how I am working or am i missusing RM for my purposes and should stick to the ncbi-blastn+?

2. Is there a way to get e-values for my RepeatMasker output scores?


thanks for any input.