I would like to detect transposon elements (I have an Annotation Track file in gff3 format) in my sRNA libraries (fasta format file).
I was able to do it using a Perl script, but it works very slowly. A colleague of mine told me that a C++ program would be faster. Is anyone able to translate the Perl script into C++?
I failed to do such transposon detection with CLC Genomics Workbench 5.5. Can anyone tell me if and how CLC can do this alignment?
Alternatively, are there any other tools that can work as I need?
I also think your question as how to "grep" the substrings (i.e, transposon sequences) by its locus parameters(gff3) from a set of fasta format string ( sRNA libraries) .
Such a thing can be divided into several parallel implementations in order to save time.
May every thing go well!
I try to explain better my problem.
I have a non-mapped sRNA library fasta file, and a transposon annotation track gff3 file. I would like to annotate fasta file with gff3 file. In other words, I would like to match records in fasta file with those in gff3 file. The aim is to count how many transposons (gff3) are present in my sRNA library (fasta).
Thanks Krzysztof. It seems good, I will try. I'm trying also to solve my problem with CLC Genomics Workbench, andnow I think to be able to do it successfully. I will let you know.
Or you can map your sRNA to the genome, and from the result use bedtool to overlap sRNA annotation with gff3 file. The you have to count how many sRNA are in that output.
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