SNAP-Zoe-Teaching

Category

Bioinformatics

Program On

Teaching

Version

20060728

Author / Distributor

SNAP-Zoe

Description

"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." More details are at SNAP-Zoe

Running Program

The last version of this application is at /usr/local/apps/eb/SNAP-Zoe/20060728-foss-2016b

To use this version, please load the module with

ml SNAP-Zoe/20060728-foss-2016b 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_SNAP-Zoe
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=SNAP-Zoe.%j.out
#SBATCH --error=SNAP-Zoe.%j.err

cd $SLURM_SUBMIT_DIR
ml SNAP-Zoe/20060728-foss-2016b
snap [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml SNAP-Zoe/20060728-foss-2016b 
snap -help
The general form of the snap command line is:

    snap <HMM file> <FASTA file> [options]

HMM file:

    The most convenient way to specify the HMM file is by name. This requires
    that the ZOE environment variable is set. In this case, snap will look
    for the HMM file in $ZOE/HMM. You may also specify the HMM file by an
    explicit path. The following are equivalent if $ZOE is in /usr/local:

        snap C.elegans.hmm ...
        snap /usr/local/Zoe/HMM/C.elegans.hmm ...
        snap worm ...  # there are a few convenient aliases in $ZOE/HMM

FASTA file:

    If you have several sequences to analyze, it is more efficient to run
    snap on a concatenated FASTA file rather than separate runs on single
    sequence files. The seqeuence may be in a compressed format

    If sequences have been masked with lowercase letters, use -lcmask to
    prevent exons from appearing in masked DNA.

Output:

    Annotation is reported to stdout in a non-standard format (ZFF). You can
    change to GFF or ACEDB with the -gff or -ace options. Proteins and
    transcripts are reported to FASTA files with the -aa and -tx options.

External definitions:

    SNAP allows you to adjust the score of any sequence model at any point
    in a sequence. This behavior is invoked by giving a ZFF file to SNAP:

        snap <hmm> <sequence> -xdef <ZFF file>

    Each feature description uses the 'group' field to issue a command:

        SET     set the score
        ADJ     adjust the score up or down
        OK      set non-cannonical scores

     >FOO
     Acceptor 120 120 + +50 . . . SET  (sets an Acceptor to 50)
     Donor    212 212 + -20 . . . ADJ  (lowers a Donor by -20)
     Inter    338 579 +  -2 . . . ADJ  (lowers Inter by -2 in a range)
     Coding   440 512 -  +3 . . . ADJ  (raises Coding by +3 in a range)
     Donor    625 638 +  -5 . . . OK   (sets range of odd Donors to -5)

If the output has scrolled off your screen, try 'snap -help | more'

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Installation

Source code is obtained from SNAP-Zoe

System

64-bit Linux