-----Messaggio originale-----

Da: GENSCAN at GeniusNet [mailto:genome@dkfz-heidelberg.de]

Inviato: martedž 18 marzo 2003 12:49

A: iacono@mailserver.unimi.it

Oggetto: GenScan Output Sequence

GENSCAN 1.0 Date run: 18-Mar-103††† Time: 12:48:51

Sequence Noname : 8460 bp : 51.00% C+G : Isochore 3 (51.00 - 57.00 C+G%)

Parameter matrix: HumanIso.smat

Predicted genes/exons:

Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..

----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------

†1.01 Init -††† 766††† 536† 231† 1† 0†† 90† 107†† 430 0.854† 43.35

†1.00 Prom -†† 2059†† 2020†† 40††††††††††††††††††††††††††††† -5.91

†2.00 Prom +†† 2474†† 2513†† 40††††††††††††††††††††††††††††† -3.81

†2.01 Init +†† 2677†† 2749†† 73† 0† 1†† 38† 115†††† 1 0.029† -0.72

†2.02 Intr +†† 6408†† 6575† 168† 1† 0†† 46†† 15†† 181 0.518†† 7.03

†2.03 Intr +†† 7204†† 7335† 132† 2† 0†† 98† 101†† 108 0.977† 14.22

†2.04 Term +†† 8209†† 8345† 137† 2† 2†† 47†† 54†† 181 0.851†† 9.09

†2.05 PlyA +†† 8450†† 8455††† 6†††††††††††††††††††††††††††††† 1.05

Predicted peptide sequence(s):

>Noname|GENSCAN_predicted_peptide_1|77_aa

MPGVKLTTQAYCKMVLHGAKYPHCAVNGLLVAEKQKPRKEHLPLGGPGAHHTLFVDCIPL

FHGTLALAPMLEVALTL

>Noname|GENSCAN_predicted_peptide_2|169_aa

MLATRVFSLVGKRAISTSVCVRAHESVVKSEDFSLPAYMDRRDHPLPEVAHVKHLSASQK

ALKEKEKASWSSLSMDEKVELYRIKFKESFAEMNRGSNEWKTVVGGAMFFIGFTALVIMW

QKHYVYGPLPQSFDKEWVAKQTKRMLDMKVNPIQGLASKWDYEKNEWKK

Explanation

Gn.Ex : gene number, exon number (for reference)

Type† : Init = Initial exon

††††††† Intr = Internal exon

††††††† Term = Terminal exon

††††††† Sngl = Single-exon gene

††††††† Prom = Promoter

††††††† PlyA = poly-A signal

S†††† : DNA strand (+ = input strand; - = opposite strand)

Begin : beginning of exon or signal (numbered on input strand)

End†† : end point of exon or signal (numbered on input strand)

Len†† : length of exon or signal (bp)

Fr††† : reading frame (a codon ending at x is in frame f = x mod 3)

Ph††† : net phase of exon (length mod 3)

I/Ac† : initiation signal or acceptor splice site score (x 10) Do/T† :

donor splice site or termination signal score (x 10) CodRg : coding

region score (x 10)

P†††† : probability of exon (sum over all parses containing exon)

Tscr† : exon score (depends on length, I/Ac, Do/T and CodRg scores)

CommentsThe SCORE of a predicted feature (e.g., exon or splice site) is

a log-odds measure of the quality of the feature based on local sequence

properties. Thus, for example, a predicted donor splice site with score

> 100 is excellent; 50-100 is acceptable; 0-50 is weak; and below 0 is

poor (probably not a real donor site).

The PROBABILITY of a predicted exon is the estimated probability under

GENSCAN's model of genomic sequence structure that the exon is correct.

This probability depends in general on global as well as local sequence

properties.† This information can be used to assess the reliability of

the predicted exon, e.g., it would be better to design PCR primers based

on a predicted exon with probability > 0.95 than one with lower

probability.