SNAP pipeline

SNAP specifications


Unique identifier OMICS_07771
Alternative name Semi-HMM-based Nucleic Acid Parser
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes



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Publication for Semi-HMM-based Nucleic Acid Parser

SNAP IN pipelines

PMCID: 5509433
PMID: 28623667
DOI: 10.7554/eLife.25783.031

[…] information (ncbi), and the chlamydomonas reinhardtii genome (merchant et al., 2007) was downloaded from phytozome (v5.5; de novo gene prediction using an a. thaliana hmm in snap yielded a set of peptide predictions (dataset 1) that served as a base for hmm alignment with pfam-a (v31.0, (, figure 6 provides a graphical representation of unique […]

PMCID: 5702742
PMID: 28837129
DOI: 10.1038/ismej.2017.139

[…] 67 bp) and for st4 3 432 010 bp (s.d. 3 131 603 bp)., we considered the 19 reconstructed genomes accounting >5 mbp for gene prediction and annotation. ad initio gene prediction was performed using snap (korf, 2004) to generate hmm models for all the sts using the available annotations to build the hmm reference profile. genome annotation was performed using maker (cantarel et al., 2008) with de […]

PMCID: 4105696
PMID: 24929829
DOI: 10.1038/ng.3012

[…] separated. stichosomes were excised from whole adult worms (n = 10, irrespective of sex), pooled and frozen, as were the posterior portions of the worms (n = 10 of each sex). all stages/tissues were snap frozen in liquid nitrogen and stored at −80 °c., total genomic dna was isolated each from a single adult male or female t. suis47,48. paired-end (insert sizes: 170 bp and 500 bp) and mate-paired […]

PMCID: 3640902
PMID: 23607900
DOI: 10.1186/1471-2164-14-270

[…] and pgt and p. triticina (pt) peptide sequences as templates for gene model discovery. the homology based gene prediction implemented in maker was integrated with the ab initio prediction program snap [44] using as training dataset the above mentioned pst, pgt, and pt datasets., illumina pair-end genomic sequence reads from each isolate were mapped onto each other isolate used as a reference […]

PMCID: 3751261
PMID: 23937194
DOI: 10.1186/1471-2105-14-243

[…] future careers may not be available – 4273π bioinformatics for biologists introduces software installation on linux through standard package management (apt), through compilation (gnu ‘make’ for snap [26] and paml [32]) and through command-line launch of a jar (modelgenerator [33] and mesquite [34]). other administrative tasks covered include upgrading linux and installing a mysql server. […]

SNAP institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK

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