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Seqping specifications

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Unique identifier OMICS_11180
Name Seqping
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Stability Alpha
Maintained Yes

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Publication for Seqping

Seqping citations

 (2)
library_books

Evidence based gene models for structural and functional annotations of the oil palm genome

2017
Biol Direct
PMCID: 5591544
PMID: 28886750
DOI: 10.1186/s13062-017-0191-4

[…] M [, ], AUGUSTUS [], and SNAP [] were trained. These HMMs were used in MAKER2 to predict oil palm genes. The initial prediction identified 45,913 gene models that were repeat-filtered. A total 17,680 Seqping gene models had significant similarities to the E. guineensis mRNA dataset and RefSeq proteins (Fig. ).The 27,915 and 17,680 gene models from Fgenesh++ and Seqping respectively were then combi […]

library_books

Seqping: gene prediction pipeline for plant genomes using self training gene models and transcriptomic data

2017
BMC Bioinformatics
PMCID: 5333190
DOI: 10.1186/s12859-016-1426-6

[…] 9 nodes (8 CPUs per node). The rice transcripts were treated as described in the Training Set Preparation section, producing 11,729 putative full-length ORFs that were then used for HMM training. The Seqping pipeline, using the new HMMs and transcriptome data identified 24,009 highly confidence rice genes. BUSCO analysis, which is a benchmarking tool to determine the completeness of genome assembl […]


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Seqping institution(s)
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Orion Genomics, St. Louis, MO, USA; School of Biosciences and Biotechnology, Faculty of Science and Technology, and Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
Seqping funding source(s)
MPOB Oil Palm Genome Programme (R009611000)

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