Output format

DESCRIPTION

The output conforms to the GFF version 2 format. For each input sequence the server prints a list of predicted splice sites, both donor and acceptor, showing their positions in the sequence and the prediction confidence scores. Only the sites with scores higher than 0.5 are predicted as splice sites and reported in the list. The sites with the scores higher than 0.8 are marked with 'H' as high confidence predictions.

The example below shows the NetUTR 1.0 output for the sequence taken from the GenBank entry X05196, containing the human aldolase C gene. The 5' UTR intron (155-1411) in that gene is predicted correctly, with high confidence.

EXAMPLE OUTPUT

##gff-version 2 ##source-version netUTR-1.0b ##date 2006-03-16 ##Type DNA # seqname source feature start end score +/- ? # --------------------------------------------------------------------------- X05196 netUTR-1.0b acceptor 512 512 0.575 + X05196 netUTR-1.0b acceptor 577 577 0.692 + X05196 netUTR-1.0b acceptor 1189 1189 0.631 + X05196 netUTR-1.0b acceptor 1411 1411 0.861 + H X05196 netUTR-1.0b acceptor 1621 1621 0.501 + X05196 netUTR-1.0b acceptor 1949 1949 0.755 + X05196 netUTR-1.0b acceptor 2378 2378 0.831 + H X05196 netUTR-1.0b acceptor 2590 2590 0.604 + X05196 netUTR-1.0b acceptor 3334 3334 0.532 + X05196 netUTR-1.0b acceptor 3692 3692 0.574 + X05196 netUTR-1.0b acceptor 5292 5292 0.522 + X05196 netUTR-1.0b donor 155 155 0.971 + H X05196 netUTR-1.0b donor 993 993 0.612 + X05196 netUTR-1.0b donor 1536 1536 0.623 + X05196 netUTR-1.0b donor 2261 2261 0.508 + X05196 netUTR-1.0b donor 2463 2463 0.604 + X05196 netUTR-1.0b donor 3335 3335 0.509 + X05196 netUTR-1.0b donor 4297 4297 0.589 + X05196 netUTR-1.0b donor 4455 4455 0.625 + X05196 netUTR-1.0b donor 5929 5929 0.616 + # ---------------------------------------------------------------------------

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