GENSCAN pipeline

GENSCAN specifications

Information


Unique identifier OMICS_01494
Name GENSCAN
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/GENSCAN

Maintainers


  • person_outline Chris Burge <>
  • person_outline Samuel Karlin <>

Publications for GENSCAN

GENSCAN citations

 (10)
2017
PMCID: 5344892

[…] identified from the kiwifruit genome database (huang et al., 2013), and four full-length myb genes highly expressed in fruit tissue were selected. the open reading frames (orfs) were predicted using genscan, and protein sequences were aligned using clustalx2.1. phylogenetic tree of myb proteins were constructed by neighbor-joining matrix with 1,000 bootstrap replicates using mega6. names […]

2015
PMCID: 4687090

[…] 1e–5 was applied to the homologue recognition. all retrieved nucleotide sequences encoding proteins with more than 50 % identity to arabidopsis or rice homologs were used for gene prediction on the genscan web server (http://genes.mit.edu/genscan.html) [41]. the predicted gene models were further examined and corrected manually through comparison with related genes in other plant species […]

2014
PMCID: 3986363

[…] [35] showed the existence of five smrdr gene loci in the s. miltiorrhiza genome. genomic dna sequences were retrieved and predicted for gene models on the genscan web server (http://genes.mit.edu/genscan.html). the five gene models computationally predicted were blast-analyzed against the non-redundant protein sequence (nr) database (http://www.ncbi.nlm.nih.gov/blast) using blastx […]

2014
PMCID: 3986363

[…] rdrs against the working draft of the s. miltiorrhiza genome (chen et al., unpublished data) using tblastn [34], [35]. the retrieved genomic dna sequences were used for gene model prediction on the genscan web server (http://genes.mit.edu/genscan.html). gene models were manually corrected according to the alignment between smrdrs and other plant rdrs obtained from blast analysis of predicted […]

2013
PMCID: 4471637

[…] 161j8 was sequenced to ∼40× coverage using roche 454 gs flx titanium technology (performed at the centre for genomic research, university of liverpool, uk). genes were predicted using blast and genscan and by alignment to known orthologous genes from other vertebrates. bac clone sequences are deposited in genbank under accession numbers kc914566–kc914567., orthology of genes encoded […]

GENSCAN institution(s)
Center for Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Mathematics, Stanford University, Stanford, CA, USA
GENSCAN funding source(s)
Supported in part by National Institutes of Health Grants 5R01GM10452-33 and 5R01HG00335-10, and National Science Foundation grant DMS9403553-002.

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