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

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

Inviato: marted́ 18 marzo 2003 11:59

A: iacono@mailserver.unimi.it

Oggetto: GenScan Output Sequence

 

 

GENSCAN 1.0 Date run: 18-Mar-103    Time: 11:58:42

 

Sequence Noname : 80520 bp : 42.66% C+G : Isochore 1 ( 0.00 - 43.00

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..

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

 

 1.15 PlyA -     27     22    6                               1.05

 1.14 Term -   1062    919  144  0  0   59   33   214 0.987   9.93

 1.13 Intr -   1386   1252  135  0  0   98  110    37 0.982   6.74

 1.12 Intr -   1658   1527  132  2  0   20  111   195 0.871  14.92

 1.11 Intr -   4042   3844  199  0  1  118    7    29 0.362  -3.77

 1.10 Intr -   7379   7203  177  1  0  130   64   110 0.661  10.91

 1.09 Intr -   8197   8113   85  2  1   70  101    76 0.996   5.06

 1.08 Intr -  16213  16096  118  1  1   69  115   110 0.900  10.92

 1.07 Intr -  16684  16557  128  2  2   39   68    89 0.606   1.48

 1.06 Intr -  16820  16793   28  2  1  113   80    37 0.839   2.17

 1.05 Intr -  20694  20541  154  2  1   82   75    78 0.700   5.05

 1.04 Intr -  25328  25171  158  2  2   90   61   142 0.928   9.59

 1.03 Intr -  25740  25638  103  2  1   63   78    99 0.994   5.66

 1.02 Intr -  28467  28355  113  0  2   87   90    74 0.993   5.76

 1.01 Init -  35126  34920  207  2  0   64   68   261 0.999  20.57

 1.00 Prom -  37705  37666   40                              -4.75

 

 2.00 Prom +  38053  38092   40                              -2.05

 2.01 Init +  40616  40676   61  1  1   69   72    50 0.701   2.96

 2.02 Term +  55758  56164  407  1  2   52   49   257 0.988  12.56

 2.03 PlyA +  56539  56544    6                               1.05

 

 3.00 Prom +  56655  56694   40                              -6.15

 3.01 Sngl +  56709  57089  381  2  0   71   39   168 0.785   6.12

 3.02 PlyA +  59006  59011    6                               1.05

 

 4.00 Prom +  67062  67101   40                              -6.35

 4.01 Sngl +  79901  80221  321  1  0   68   55   244 0.823  14.84

 4.02 PlyA +  80435  80440    6                              -0.45

 

 

Predicted peptide sequence(s):

 

 

>Noname|GENSCAN_predicted_peptide_1|626_aa

MEHIQGAWKTISNGFGFKDAVFDGSSCISPTIVQQFGYQRRASDDGKLTDPSKTSNTIRV

FLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLHEHKGKKARLDWNTDAAS

LIGEELQVDFLDHVPLTTHNFARKTFLKLAFCDICQKFLLNGFRCQTCGYKFHEHCSTKV

PTMCVDWSNIRQLFSQHRYSTPHAFTFNTSSPSSEGSLSQRQRSTSTPNVHMVSTTLPVD

SRMIEDAIRSHSESASPSALSSSPNNLSPTGWSQPKTPVPAQRERAPVSGTQEKNKIRPR

GQRDSSYYWEIEASEVMLSTRIGSGSFGTVYKGKWHGDVAVKILKVVDPTPEQFQAFRNE

VAVLRKTRHVNILLFMGYMTKDNLAIVTQWCEGSSLYKHLHVQETKFQMFQLIDIARQTA

QGMDYLHAKNIIHRDMKSNSILWLLSSFDCSVLNLGKQKGGFLSQVALGARGYLFKERGR

GQENRKVRKLAPEVIRMQDNNPFSFQSDVYSYGIVLYELMTGELPYSHINNRDQIIFMVG

RGYASPDLSKLYKNCPKAMKRLVADCVKKVKEERPLFPQILSSIELLQHSLPKINRSASE

PSLHRAAHTEDINACTLTTSPRLPVF

 

>Noname|GENSCAN_predicted_peptide_2|155_aa

MLKYADNAASRALQVVSGKRVSEVLARAIRQEKEIKGIQLGKEEVKLSLFADDMIVYLEN

LIVSAQNLLKLTGNFSKVSGYKINVQKSQAFLYTNNRQTESQIMSELSFTIASKRIKYLG

IRLTRDVKDLFKENYKPLLNKIKEDTNGRTFHAHG

 

>Noname|GENSCAN_predicted_peptide_3|126_aa

MGKDFMTKTPKARATKAQIDKWDLIKLKSFCTAKETTITVNTQPTEWEKIFAIYPSDKGL

ISSIYKELKQIYKKKIKQPHQKVGKGYEQTLLKRHSCRQQTHEKMLITGHQRNANQNHND

IPSHTS

 

>Noname|GENSCAN_predicted_peptide_4|106_aa

MGQLWADFPTAKYEECAWHKGGVGTFPPNTRKFEWDVGTRLAGHDTGLRGPRPTLPQGDN

GLAQALCPAAAGPLHQRHPGPVALEADPSAPPPGSPGIHDPVLPPT

 

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.

 

 

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