SNAP: gene finding for both eukaryotic and prokaryotic genomes.

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SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.

References:

Korf I.
Gene finding in novel Genomes.
BMC Bioinformatics (2004), 5:59

Documentation

SNAP Github page

Important Notes

Module Name: SNAP (see the modules page for more information)
Unusual environment variables set
- SNAP_HOME SNAP installation directory
- SNAP_BIN SNAP executable directory
- SNAP_SRC a folder containing the source code
- SNAP_DATA a folder containing sample data
- SNAP_HMM a folder containing sample Hidden Markov Models

Interactive job

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn4471 ~]$module load snap

The bin directory of the application includes three executable files: gcng_train.py, gcng_predict.py and gcng_visualize.py. In order to display the usage message and available command line options for an executable, type its name followed by the option "-h". For example:

[user@cn4471 ~]$snap 

SNAP - Semi-HMM-based Nucleic Acid Parser (version 2006-07-28)

usage: snap [options]   [options]
options:
  -help           report useful information
  -lcmask         treat lowercase as N
  -plus           predict on plus strand only
  -minus          predict on minus strand only
  -gff            output annotation as GFF
  -ace            output annotation as ACED
  -quiet          do not send progress to STDERR
  -aa       create FASTA file of proteins
  -tx       create FASTA file of transcripts
  -xdef     external definitions
  -name   name for the gene [default snap]
[user@cn4471 ~]$ cp $SNAP_DATA/* .
[user@cn4471 ~]$ snap $SNAP_HMM/worm worm.dna.gz 
scoring.....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring.....decoding.10.20.30.40.50.60.70.80.90.100 done
>F56C11.1
Einit   1487    1493    +       5.285   0       1       1       F56C11.1-snap.1
Exon    2140    2217    +       24.843  2       1       2       F56C11.1-snap.1
Exon    2267    2380    +       -8.866  2       1       0       F56C11.1-snap.1
Exon    2475    2864    +       23.338  2       1       1       F56C11.1-snap.1
Exon    2911    3114    +       16.891  2       1       2       F56C11.1-snap.1
Exon    3162    3413    +       24.850  2       1       1       F56C11.1-snap.1
Exon    3460    3751    +       42.990  2       2       2       F56C11.1-snap.1
Exon    4146    4359    +       51.685  1       0       0       F56C11.1-snap.1
Exon    4437    4593    +       13.882  0       1       2       F56C11.1-snap.1
Exon    4638    5086    +       30.213  2       0       1       F56C11.1-snap.1
Exon    5132    5429    +       42.745  0       1       1       F56C11.1-snap.1
Exon    6003    6300    +       31.135  2       2       1       F56C11.1-snap.1
Exon    6348    6517    +       19.107  1       1       0       F56C11.1-snap.1
Exon    6561    6760    +       11.674  2       0       1       F56C11.1-snap.1
Exon    7597    7721    +       14.702  0       2       0       F56C11.1-snap.1
Exon    7826    8036    +       21.887  1       0       2       F56C11.1-snap.1
Exon    8089    8766    +       40.264  0       0       0       F56C11.1-snap.1
Exon    8896    9027    +       23.658  0       0       0       F56C11.1-snap.1
Eterm   9072    9197    +       21.423  0       0       2       F56C11.1-snap.1
[user@cn4471 ~]$ snap $SNAP_HMM/thale thale.dna.gz 
scoring.....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring.....decoding.10.20.30.40.50.60.70.80.90.100 done
>At1g01040.0
Einit   1007    1954    +       85.269  0       0       1       At1g01040.0-snap.1
Exon    2024    2137    +       8.926   0       0       1       At1g01040.0-snap.1
Exon    2234    2444    +       20.788  0       1       1       At1g01040.0-snap.1
Exon    2523    2917    +       35.162  2       0       1       At1g01040.0-snap.1
Exon    3006    3225    +       34.428  0       1       2       At1g01040.0-snap.1
Exon    3307    3479    +       14.790  2       0       2       At1g01040.0-snap.1
Exon    3563    3685    +       4.678   0       0       1       At1g01040.0-snap.1
Exon    3774    3934    +       10.179  0       2       2       At1g01040.0-snap.1
Exon    4025    4258    +       25.991  1       2       2       At1g01040.0-snap.1
Exon    4344    4506    +       4.289   1       0       0       At1g01040.0-snap.1
Exon    4581    4763    +       28.696  0       0       2       At1g01040.0-snap.1
Exon    4854    5015    +       15.217  0       0       2       At1g01040.0-snap.1
Exon    5100    5195    +       23.205  0       0       2       At1g01040.0-snap.1
Eterm   5285    5917    +       45.878  0       0       1       At1g01040.0-snap.1
Einit   6086    6144    +       6.596   0       2       1       At1g01040.0-snap.2
Exon    6190    6287    +       22.495  1       1       1       At1g01040.0-snap.2
Exon    6372    6562    +       17.809  2       0       1       At1g01040.0-snap.2
Exon    6642    6803    +       16.407  0       0       2       At1g01040.0-snap.2
Exon    6828    7547    +       69.159  0       0       2       At1g01040.0-snap.2
Exon    7629    7793    +       40.262  0       0       2       At1g01040.0-snap.2
Exon    7892    8298    +       46.310  0       2       1       At1g01040.0-snap.2
Eterm   8384    8561    +       17.079  1       0       2       At1g01040.0-snap.2

End the interactive session:

[user@cn4471 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$