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GMAP specifications

Information


Unique identifier OMICS_15072
Name GMAP
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Source code URL http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-01-14.tar.gz
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Thomas Wu

Publication for GMAP

GMAP citations

 (159)
library_books

Parallel evolution of Batesian mimicry supergene in two Papilio butterflies, P. polytes and P. memnon

2018
Sci Adv
PMCID: 5906075
PMID: 29675466
DOI: 10.1126/sciadv.aao5416

[…] rosophila melanogaster, Apis mellifera, and Tribolium castaneum. RNA-seq–based gene prediction was performed using TopHat (version 2.1.0) (), Cufflinks (version 2.2.1) (), Trinity (version 2.2.0) (), GMAP (version 2016-06-30) (), and TransDecoder (version 3.0.0; http://transdecoder.github.io/). A MAKER gene was replaced if its exons were covered by an RNA-seq–based gene covered MAKER exons (covera […]

library_books

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

2018
BMC Genomics
PMCID: 5902842
PMID: 29661190
DOI: 10.1186/s12864-018-4656-3

[…] s was performed as follows. The published gene models for ‘Hongyang’ [] and A. chinensis ESTs within NCBI GenBank were downloaded and mapped to the assembled pseudo-chromosome sequences of Red5 using GMAP (version 2014–10-22) []. The sequences of the Red5 pseudo-chromosomes were repeat masked using RepeatMasker (version open-4.0.5) with options “-e ncbi -pa 30 -s -nolow -species viridiplantae -a - […]

library_books

Ginseng Genome Database: an open access platform for genomics of Panax ginseng

2018
BMC Plant Biol
PMCID: 5898050
PMID: 29649979
DOI: 10.1186/s12870-018-1282-9

[…] embled transcriptome structure’ and ‘repeats’. In addition, the alignments of RNA-Seq reads to the genome sequence generated directly from Binary Alignment/MAP (BAM) and PacBio contig alignment using GMAP [] were also incorporated to perk up the structural annotation of the gene. Furthermore, protein sequences of non-coding genes including microRNA (miRNA) and long non-coding RNAs (lncRNA) can be […]

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

[…] first aligned to the genome assembly 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 […]

call_split

A large scale multiomics analysis of wheat stem solidness and the wheat stem sawfly feeding response, and syntenic associations in barley, Brachypodium, and rice

2018
PMCID: 5908820
PMID: 29470681
DOI: 10.1007/s10142-017-0585-5
call_split See protocol

[…] uctions, and sequencing was performed using an Illumina Hi-Seq 2000 platform. The RNA-Seq reads were trimmed using Sickle (v.1.33) before being aligned to the T. aestivum chromosome 3B assembly using GMAP (v.2017-02-25; Wu and Watanabe ). The aligned reads were then compared to a GFF file containing annotated transcripts of T. aestivum (variety Chinese Spring) and the read counts were obtained usi […]

library_books

De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust

2018
MBio
PMCID: 5821079
PMID: 29463655
DOI: 10.1128/mBio.01650-17

[…] (ii) protein evidence from a UniProtKB/Swiss-Prot-curated database (downloaded on 26 April 2017) was aligned to the genomes using TBLASTN and exonerate (), (iii) transcript evidence was aligned using GMAP (), (iv) ab initio gene predictors AUGUSTUS v3.2.3 () and GeneMark-ET v4.32 () were trained using BRAKER1 (), (v) tRNAs were predicted with tRNAscan-SE (), (vi) consensus protein coding gene mode […]

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GMAP institution(s)
Department of Bioinformatics, Genentech, Inc, South San Francisco, CA, USA; Department of Corporate Information Technology, Genentech, Inc, South San Francisco, CA, USA

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