GMAP: a genomic mapping and alignment program for mRNA and EST sequence

By Thomas D. Wu, Colin K. Watanabe. Bioinform., 2005

2,236 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/43546f35f8853dbaab3232a9561254a506ea53bb

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

A hitchhiker's guide to expressed sequence tag (EST) analysis (2006, methodology): “BLAT, GMAP and MGALIGN are considered to be reliable methods for this process [56].”
Computational methods for transcriptome annotation and quantification using RNA-seq (2011, neutral): “Alignment of reads is a classic problem in bioinformatics with several solutions specifically for EST mapping 8,9 .”
Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis (2012, methodology): “Th ese SNPs were then mapped to a location on the TGI scaff olds by aligning the contigs with GMAP (Wu and Watanabe, 2005) and calculating the genomic position with a Perl script.”
proovread: large-scale high-accuracy PacBio correction through iterative short read consensus (2014, methodology): “During the assessment the corrected LRs were remapped onto the reference sequence by GMAP (Wu and Watanabe, 2005).”
A highly conserved program of neuronal microexons is misregulated in autistic brains (2014, background): “In particular, microexons (Beachy et al., 1985; Coleman et al., 1987), defined here as 3–27 nucleotide (nt)-long exons, have been largely missed by genome annotations and transcriptome profiling studies (Volfovsky et al., 2003; Wu et al., 2013; Wu and Watanabe, 2005).”
The genome of the blood fluke Schistosoma mansoni (2009, background): “mansoni EST data set, which comprises ESTs from the following developmental stages: germball (28,497), cercaria (21,639), 3-day somule (6,122), 7-day somule (41,043), 21-day liver worm (6,044), 28-day liver worm (11,227), 45-day adult worm (59,552), egg (33,674) and miracidium (19,982).”
TopHat: discovering splice junctions with RNA-Seq (2009, positive): “The sensitivity of the Velvet+GMAP method is shown in Figure 4.”