PASA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PASA

Tool usage distribution map

This map represents all the scientific publications referring to PASA per scientific context
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Associated diseases

This word cloud represents PASA usage per disease context

Popular tool citations

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PASA specifications


Unique identifier OMICS_20215
Alternative name Program to Assemble Spliced Alignments
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A targeted genome and some transcripts.
Input format FASTA
Operating system Unix/Linux, Mac OS
Programming languages C++, Perl
Computer skills Advanced
Version 2.1.0
Stability Stable
Source code URL
Maintained Yes


  • Invertebrates
    • Plasmodium falciparum
  • Plants and Fungi
    • Arabidopsis thaliana
    • Aspergillus fumigatus
    • Oryza sativa
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus




No version available



  • person_outline Brian Haas

Publication for Program to Assemble Spliced Alignments

PASA citations


Whole genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044

[…] d genome using TopHat2 [], which generated evidence of splice sites, introns, and exons. Additionally, Trinity (Trinity, RRID:SCR_013048), version 2.0.6, [], was utilized to assemble transcripts, and PASA (version 2.0.0) [] was used to group alternatively spliced isoforms. For the ab initio gene prediction, the standard Augustus (version 3.0.3) pipeline was used to yield potentially predicted gene […]


Analysis of Theileria orientalis draft genome sequences reveals potential species level divergence of the Ikeda, Chitose and Buffeli genotypes

BMC Genomics
PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2

[…] eneMark ET (Robertson and Fish Creek), and GeneMark ES (Goon Nure). A training set based on EST alignments (RNA data sourced from the Shintoku WGS project []) and transcoding regions was generated by PASA v2.1.0 [] and used to train all ab initio predictors except GeneMark ES. Alignment of EST and protein evidence was performed with Exonerate v2.2.0 [] using the coding2genome and protein2genome mo […]


The Gastrodia elata genome provides insights into plant adaptation to heterotrophy

Nat Commun
PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] ), GeneScan (version 1.0), GlimmerHMM (version 3.0.1), and SNAP (version) were also used to predict coding regions in the repeat-masked genome. Of these, Augustus, SNAP and GlimmerHMM were trained by PASA-H-set gene models. Gene models generated from all the methods were integrated by EvidenceModeler (EVM). Weights for each type of evidence were set as follows: PASA-T-set > Homology-set > Cufflink […]


A Possible Trifunctional β Carotene Synthase Gene Identified in the Draft Genome of Aurantiochytrium sp. Strain KH105

PMCID: 5924542
PMID: 29642531
DOI: 10.3390/genes9040200
call_split See protocol

[…] 1) were performed using ab initio and complementary DNA (cDNA) sequence alignment prediction derived from Augustus software []. Assembled Aurantiochytrium transcriptome sequences were processed with PASA [], and the 500 longest ORFs were used to train the prediction software. Assembled Illumina RNA sequencing (RNA-seq) data were aligned to the assembled genome and incorporated as an Augustus “hin […]


The draft genome sequence of forest musk deer (Moschus berezovskii)

PMCID: 5906906
PMID: 29635287
DOI: 10.1093/gigascience/giy038

[…] anscriptome-based prediction, musk gland RNA-seq data were assembled using Trinity (Trinity, RRID:SCR_013048) with genome guide and de novo mode, respectively. The gene structures were obtained using PASA pipeline (version 2.0.2) []. We used EVM (version 1.1.1) to integrate the above evidence and obtained a consensus gene set []. Apollo (version 1.11.6) was performed to manually inspect gene struc […]


Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

BMC Genomics
PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] y by GSNAP v.2014.7.21 [] to generate a BAM file as the input. The resulting transcripts from these two modes were combined and aligned to the genome assembly with GMAP v.2014.7.21 [] incorporated in Program to Assemble Spliced Alignments (PASA) pipeline v.2.0.2 [] to build a complete set of transcripts. Homologs from predicted proteins of H. irregulare TC 32–1 available in Mycocosm at Joint Genom […]

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PASA institution(s)
J Craig Venter Institute, The Institute for Genomic Research, Rockville, MD, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, College Park, MD, USA; Computation Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA; Institute for Genome Sciences, University of Maryland Medical School, Baltimore, MD, USA; Department of Plant Biology, Michigan State University, East Lansing, MI, USA
PASA funding source(s)
Supported by a National Science Foundation Plant Genome Research Program grant (DBI-0321538); by NIH grant R01-LM006845 and by MSC contract NIH-N01-AI-30071.

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