I was curious if anyone has heard of or utilized the target restricted assembly method (TRAM) as outlined in Johnson et al. (2010)? My lab is currently looking into using this approach for a phylogenomic project and has some questions regarding the protocol.
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It's always a good idea to provide a hyperlink in addition to a somewhat truncated citation
I have to chuckle that they published this -- good that it attracts some attention, but many groups (including the one I was in at Millennium) were doing this well over a decade ago as a way to mine interesting things from unassembled genomes.
The approach is straightforward, so perhaps you should post what is causing you difficulty.
1) Format the NGS reads as a BLASTable database
2) TBLASTN them with your query protein(s)
3) Retrieve the corresponding reads. If the reads were paired end, then for each hit sequence retrieve its pair as well
4) Assemble the reads with your favorite assembler.
5) TBLASTN again to annotate your proteins in the assembled reads.
You can also use your assembled contigs to BLASTN the dataset to find more reads for assembling & cycle through this a few times; this can sometimes drive your contigs together if you care about intron sizes.
With BioPerl, BioPython or similar libraries, you should be able to get this process up-and-running in a few pages of code.
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