I have a eukaryotic protein sequence and the corresponding contig containing the gene. I would like to recover the cDNA sequence (i.e. only the exons spliced together) . Are there any tools to do this? tblastn only gives me the fragments, but doesn't piece them together.
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Michael Kuhn
I have used both exonerate and NAP-AAT. They work reasonably well, especially when the protein is derived from this contig.
I would like to mention a recent paper on this by Gotoh, which reviews some of the softwares, as well as his new software.
Thanks a lot for the answer! Exonerate works fine for my purposes with this command line: "exonerate --model protein2genome query.fa contig.fna --ryo ">%ti (%tab - %tae)n%tcsn" | less"
Take a look at Wise2, although it's not a perfect match as it only aligns protein sequences with contigs and you have to extract the exons yourself.
is there a modern equivalent to blastwise?
I have never used blastwise.
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