ESTmapper statistics

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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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Maintainers


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

Publications for ESTmapper

ESTmapper in publications

 (9)
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 […]

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 […]

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

[…] [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 […]

PMCID: 2688933
PMID: 19393038
DOI: 10.1186/gb-2009-10-4-r42

[…] 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 […]

PMCID: 2639302
PMID: 18952627
DOI: 10.1093/bioinformatics/btn548

[…] (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, […]


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

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