PASA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PASA
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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
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Popular tool citations

chevron_left Protein-coding gene prediction Assembly reconciliation Pairwise sequence alignment chevron_right
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Protocols

PASA specifications

Information


Unique identifier OMICS_20215
Name PASA
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 https://codeload.github.com/PASApipeline/PASApipeline/zip/v2.1.0
Maintained Yes

Taxon


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

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Versioning


No version available

Documentation


Maintainer


  • person_outline Brian Haas

Publication for Program to Assemble Spliced Alignments

PASA citations

 (128)
library_books

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

2018
GigaScience
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 […]

library_books

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

2018
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 […]

library_books

The Gastrodia elata genome provides insights into plant adaptation to heterotrophy

2018
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 […]

call_split

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

2018
Genes
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 […]

library_books

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

2018
GigaScience
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 […]

library_books

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

2018
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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