Gene prediction software
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README.md

SNAP Documentation

Introduction

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.

Reference

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

Contact

I appreciate bug reports, comments, and suggestions. My current contact information is:

License

This software is covered by the GNU General Public License. The license is included with the software and is available from www.gnu.org.

Files and Directories

DNA               Contains some sample sequences
HMM               Contains SNAP parameter files
LICENSE           The GNU General Public License
Makefile          For compiling
Makefile.include  Automatically generated, should not be edited
Zoe               A library containing lots of the base functions
fathom.c          Utility for investigating sequences and annotation
forge.c           Parameter estimation
hmm-assembler.pl  Creates HMMs for SNAP
snap.c            Gene prediction program

Your favorite genome...

If you wish to train SNAP for a new genome, please contact me. Parameter estimation is not particularly difficult, but the procedure is not well documented and I have only included the minimum applications here. I've included the basic strategy at the end of this document.

INSTALLATION INSTRUCTIONS

The software is routinely compiled and tested on Mac OS X. It should compile fine on any Linux/Unix type operating systems but new compilers sometimes complain, so please let me know if you have problems.

Enviroment

The ZOE environment variable can be used by SNAP to find the HMM files. Set this to the directory containing this file. For example, if you unpackaged the tar-ball in /usr/local, set the ZOE environment variable to /usr/local/Zoe

setenv ZOE /usr/local/Zoe # csh, tcsh, etc
export ZOE=/usr/local/Zoe # sh, bash, etc

If you do not use the ZOE environment variable, you can still use SNAP but you must specify the explict path to the parameter file.

Compiling

Provided you have gcc and make, compiling should be as simple as:

make

Testing

./snap HMM/thale DNA/thale.dna.gz
./snap HMM/worm DNA/worm.dna.gz

PARAMETER ESTIMATION

Sequences must be in FASTA format. It's a good idea if you don't have genes that are too related to each other.

Gene structures must be in ZFF format. What is ZFF? It is a non-standard format (ie. nobody uses it but me) that bears resemblence to FASTA and GFF (both true standards). There are two styles of ZFF, the short format and the long format. In both cases, the sequence records are separated by a definition line, just like FASTA. In the short format, there are 4 fields: Label, Begin, End, Group. The 4th field is optional. Label is a controlled vocabulary (see zoeFeature.h for a complete list). All exons of a gene (or more appropriately a transcriptional unit) must share the same unique group name. The strand of the feature is implied in the coordinates, so if Begin > End, the feature is on the minus strand. Here's and example of the short format with two sequences, each containing a single gene on the plus strand:

>sequence-1
Einit    201    325   Y73E7A.6
Eterm   2175   2319   Y73E7A.6
>sequence-2
Einit    201    462   Y73E7A.7
Exon    1803   2031   Y73E7A.7
Exon    2929   3031   Y73E7A.7
Exon    3467   3624   Y73E7A.7
Exon    4185   4406   Y73E7A.7
Eterm   5103   5280   Y73E7A.7

The long format adds 5 fields between the coordinates and the group: Strand, Score, 5'-overhang, 3'-overhang, and Frame. Strand is +/-. Score is any floating point value. 5'- and 3'-overhang are the number of bp of an incomplete codon at each end of an exon. Frame is the reading frame (0..2 and not 1..3). Here's an example of the long format:

>Y73E7A.6
Einit    201    325   +    90   0   2   1   Y73E7A.6
Eterm   2175   2319   +   295   1   0   2   Y73E7A.6
>Y73E7A.7
Einit    201    462   +   263   0   1   1   Y73E7A.7
Exon    1803   2031   +   379   2   2   0   Y73E7A.7
Exon    2929   3031   +   236   1   0   0   Y73E7A.7
Exon    3467   3624   +   152   0   2   0   Y73E7A.7
Exon    4185   4406   +   225   1   2   2   Y73E7A.7
Eterm   5103   5280   +    46   1   0   2   Y73E7A.7

The most important part of parameter estimation is preparing a training set. There are many ways to go about this. At the end, you want these in the ZFF short format. Save the ZFF as genome.ann and the FASTA as genome.dna. The first step is to look at some features of the genes:

fathom genome.ann genome.dna -gene-stats 

Next, you want to verify that the genes have no obvious errors:

fathom genome.ann genome.dna -validate

You may find some errors and warnings. Check these out in some kind of genome browser and remove those that are real errors. Next, break up the sequences into fragments with one gene per sequence with the following command:

fathom -genome.ann genome.dna -categorize 1000

There will be up to 1000 bp on either side of the genes. You will find several new files.

alt.ann, alt.dna (genes with alternative splicing)
err.ann, err.dna (genes that have errors)
olp.ann, olp.dna (genes that overlap other genes)
wrn.ann, wrn.dna (genes with warnings)
uni.ann, uni.dna (single gene per sequence)

Convert the uni genes to plus stranded with the command:

fathom uni.ann uni.dna -export 1000 -plus

You will find 4 new files:

export.aa   proteins corresponding to each gene
export.ann  gene structure on the plus strand
export.dna  DNA of the plus strand
export.tx   transcripts for each gene

The parameter estimation program, forge, creates a lot of files. You probably want to create a directory to keep things tidy before you execute the program.

mkdir params
cd params
forge ../export.ann ../export.dna
cd ..

Last is to build an HMM.

hmm-assembler.pl my-genome params > my-genome.hmm

There are a number of options for forge and hmm-assembler.pl that I have not described here. Hopefully I'll document these one day.