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SPLM - Prediction of splice sites in Human DNA sequences

The program developed by Salamov A and Solovyev V. It locates potential splice site positions based on 5 weight matrices for donor sites and a model including dinucleotide composition and weight matrixfor acceptor splice site. Program includes prediction of potential GC -donor sites and non-standard splice sites as AT-AC

Program does not EXCLUDE splice sites close to sites predicted with higher scores or sites on different chains. User could make processing based on the reported scores. It designed to be useful to analyze ALTERNATIVE Splice variants and NON-CANONICAL splice sites. Program has much higher number of overpredicted sites comparing with SPL program.

Some description see at:

Solovyev V.V. (2001)
Statistical approaches in Eukaryotic gene prediction. In Handbook of Statistical genetics (eds. Balding D. et al.),
John Wiley & Sons, Ltd., p. 83-127.

Threshold values are from 1 to 100. For example, value 30 means that threshold set on the level which detects 30% of highest scoring sites from the database of all known splice sites.
Score 20 means that this site has score better than bottom 20% of score-ordered known sites.

 
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Example of output:
splm  Wed Apr 11 23:16:32 EDT 2001
 Prediction of splice sites on Human sequences
 Length of sequence   2040
Number of Donor    sites:     10 Threshold:   90
    1     130      68   -   GT
    2     463      14   +   GT
    3     642      26   +   GT
    4     710      12   +   GT
    5     845      30   +   GT
    6     962      55   -   GT
    7    1024      48   +   GT
    8    1255      22   +   GT
    9    1363      42   +   GT
   10    2029      70   +   GT
Number of Acceptor sites:     29 Threshold:   90
    1      23      43   -   AG
    2     131      13   -   AG
    3     188      13   -   AG
    4     191      91   -   AG
    5     314      44   -   AG
    6     359      14   -   AG
    7     380      29   -   AG
    8     446      74   -   AG
    9     499      14   -   AG
   10     704      15   -   AG
   11     805      19   -   AG
   12     839      39   -   AG
   13     900      14   -   AG
   14     925       9   -   AC
   15     940      26   -   AG
   16    1065      93   +   AG
   17    1401      36   +   AG
   18    1488      80   +   AG
   19    1542      41   +   AG
   20    1593      62   +   AG
   21    1626      49   +   AG
   22    1637      18   -   AG
   23    1674      32   +   AG
   24    1708      41   +   AG
   25    1786      11   +   AG
   26    1825      15   +   AG
   27    1859      84   +   AG
   28    2003      13   +   AG
   29    2020      23   -   AG
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