ESTmapper statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ESTmapper

Tool usage distribution map

This map represents all the scientific publications referring to ESTmapper per scientific context
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ESTmapper specifications


Unique identifier OMICS_29041
Name ESTmapper
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Maintained Yes




No version available


  • person_outline Xue Wu
  • person_outline Woei-Jyh Lee
  • person_outline Chau-Wen Tseng

Publications for ESTmapper

ESTmapper citations


Evaluation of Genome Sequencing Quality in Selected Plant Species Using Expressed Sequence Tags

PLoS One
PMCID: 3726750
PMID: 23922843
DOI: 10.1371/journal.pone.0069890

[…] To map EST sequences to a genome and promote research advances in EST alignment on genome, est_genome, dds/gap2, sim4, Spidey, GeneSeqer, MGAlign, est2genome (a software of EMBOSS packet), GMAP, and ESTmapper softwares – have also been introduced.These EST sequences, public genome sequences and bioinformatics tools provide a possible way to evaluate the quality of multiple plant genome sequencing […]


A Hybrid Distance Measure for Clustering Expressed Sequence Tags Originating from the Same Gene Family

PLoS One
PMCID: 3469558
PMID: 23071763
DOI: 10.1371/journal.pone.0047216

[…] be transcript-based (EST-EST) or genome-based (EST-Genome). Transcript-based alignment compares similarities among ESTs, where BLAST or its variant can be used to accomplish the task. PaCE , GMAP , ESTMapper , ECgene , and EasyCluster are attached to genome-based alignment. These clustering tools generate better clustering quality as compared to the transcript-based, but these tools are only op […]


Mechanisms of intron gain and loss in Drosophila

BMC Evol Biol
PMCID: 3296678
PMID: 22182367
DOI: 10.1186/1471-2148-11-364

[…] database [GenBank:PRJNA163] []. The annotation of A. gam was generated by mapping mRNA sequences back onto A. gam' was generated by mapping mRNA sequences back onto A. gams's genome using the program ESTMapper []. Orthologs were identified using the FASTA program and extracting reciprocal best hits with e-value ≤ 10-30, similarity ≥ 60% and query sequence coverage ≥ 60%. If an ortholog was found i […]


Genome Assembly Has a Major Impact on Gene Content: A Comparison of Annotation in Two Bos Taurus Assemblies

PLoS One
PMCID: 3120881
PMID: 21731731
DOI: 10.1371/journal.pone.0021400

[…] Transcript sequences from one assembly were mapped to the other assembly using ESTmapper , retaining all alignments longer than 100 bp with 95% or higher sequence identity. ESTmapper maps large cDNA sequence data sets to a target genome in two stages: for each query sequence, fi […]


A whole genome assembly of the domestic cow, Bos taurus

Genome Biol
PMCID: 2688933
PMID: 19393038
DOI: 10.1186/gb-2009-10-4-r42
call_split See protocol

[…] omoted from experimentally validated sequences and identified with the code 'provisional' were retained. Sequences were aligned to the BCM4 and the UMD2 genomes using the high-throughput mapping tool ESTmapper [,], retaining all spliced alignments longer than 100 bp and with ≥ 95% sequence identity as significant. This procedure produced 12,069 alignments for 8,555 genes on the BCM4 genome and 12, […]


Aggressive assembly of pyrosequencing reads with mates

PMCID: 2639302
PMID: 18952627
DOI: 10.1093/bioinformatics/btn548
call_split See protocol

[…] r ( Repeat annotation was generated with REPuter (Kurtz et al., ) with a post-process to aggregate repeat classes by overlapping sequence. EST alignments were generated with the ESTmapper ( extension to Sim4 (Florea et al., ).Reference: the Psychromas sp. CNPT3 reference (RefSeq NZ_AAPG00000000), with 2 945 265 bases in one linear contig, had been produced […]

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ESTmapper institution(s)
Department of Computer Science, University of Maryland at College Park, MD, USA

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