Hi!
I have resequenced two strains of the same bacteria using 454 data. It seems that the run was rather crappy, and I got a lot of homopolymer errors (in average 1 frameshift per gene). I need to get rid of those errors, without doing any further sequencing. My purpose is to compare substitution rates in these strains, so I don't really need extra-accurate sequences.
For the moment, my strategy is the following:
- Use the reference strain genes as a query with BLAST-Extend-Repraze (BER, http://ber.sourceforge.net/) tool.
- Parse the output of this (which seems not quite straightforward).
- Remove extra nucleotides in my sequence, or add Ns.
Shortly, BER takes the output of a regular blastp of your favorite protein, retrieves hits that match nicely against it, goes back to the DNA sequence corresponding to your protein (i.e, the CDS + some flanking sequence).
Is there any other tool that I'm not aware of? Do you know any BER output parser? Does my strategy make sense to you?
Thanks for your advice and comments!
I have resequenced two strains of the same bacteria using 454 data. It seems that the run was rather crappy, and I got a lot of homopolymer errors (in average 1 frameshift per gene). I need to get rid of those errors, without doing any further sequencing. My purpose is to compare substitution rates in these strains, so I don't really need extra-accurate sequences.
For the moment, my strategy is the following:
- Use the reference strain genes as a query with BLAST-Extend-Repraze (BER, http://ber.sourceforge.net/) tool.
- Parse the output of this (which seems not quite straightforward).
- Remove extra nucleotides in my sequence, or add Ns.
Shortly, BER takes the output of a regular blastp of your favorite protein, retrieves hits that match nicely against it, goes back to the DNA sequence corresponding to your protein (i.e, the CDS + some flanking sequence).
Is there any other tool that I'm not aware of? Do you know any BER output parser? Does my strategy make sense to you?
Thanks for your advice and comments!
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