Online documentation for SNAP is sparse, what follows is the contents of the
README file that accompanies the source code.
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.
Korf I. Gene finding in novel Genomes. BMC Bioinformatics 2004, 5:59
I appreciate bug reports, comments, and suggestions. My current contact information is:
email: email@example.com web: http://homepage.mac.com/iankorf
This software is covered by the GNU General Public License. The license is included with the software and is available from www.gnu.org.
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 fathom.c Utility for investigating sequences and annotation forge.c Parameter estimation hmm-assembler.pl Creates HMMs for SNAP snap.c Gene prediction program zoe* Sources from the ZOE library
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.
The software is routinely compiled and tested on Mac OS X. It should compile fine on any Linux/Unix type operating systems.
The ZOE environment variable is 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 or 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.
The source code is all ANSI compliant and should compile without problems. Please contact me if you have troubles. The default compiler is gcc. If you have gcc installed, the easiest is to just compile as:
I have also included some specific architectures which may produce faster code. See the Makefile for details.
./snap HMM/thale DNA/thale.dna.gz ./snap HMM/worm DNA/worm.dna.gz
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.