Question about Exonerate output

I am running a protein2genome allignment on exonerate, and this is the result I receive (vulgar format):

vulgar: protein2 0 626 . dna_1 1380 3258 + 3359 M 626 1878
>dna_1 (1380 - 3258)

vulgar: protein1 0 485 . dna_2 1200 2908 + 2400 M 48 144 S 0 2 5 0 2 I 0 146 3 0 2 S 1 1 M 67 201 5 0 2 I 0 99 3 0 2 M 369 1107
>dna_2 (1200 - 2908)

vulgar: protein1 43 102 . dna_2 188 11 - 140 M 59 177
>dna_2 (188 - 11)
`

The last result happens to be on the minus strand, however it is not a complete hit. "Protein1" has 485 aa-s, where as the last hit has a location of 188 : 11.

Is it possible to tell exonerate somehow not to show such incomplete hits?

exonerate alignment genome protein

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updated 4.4 years ago by Ram

• written 11.6 years ago by lumramabaja •

1 answer

Better late than never. One way to clean up the output would be to apply a score filter using the --percent option, another could be to turn off reporting of suboptimal alignments with --subopt FALSE. Otherwise, one can always postprocess the output.

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written 6.7 years ago by Jean-Karim Heriche