ESTmapper statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ESTmapper
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Tool usage distribution map

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

ESTmapper specifications

Information


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

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Versioning


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Maintainers


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

Publications for ESTmapper

ESTmapper citations

 (10)
library_books

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

2013
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 […]

library_books

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

2012
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 […]

library_books

Mechanisms of intron gain and loss in Drosophila

2011
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 […]

library_books

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

2011
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 […]

call_split

A whole genome assembly of the domestic cow, Bos taurus

2009
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, […]

call_split

Aggressive assembly of pyrosequencing reads with mates

2008
Bioinformatics
PMCID: 2639302
PMID: 18952627
DOI: 10.1093/bioinformatics/btn548
call_split See protocol

[…] r (http://emboss.sf.net). 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 (http://kmer.sf.net) 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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