GENSCAN protocols

GENSCAN specifications


Unique identifier OMICS_01494
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


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

Publications for GENSCAN

GENSCAN IN pipelines

PMCID: 5344892
PMID: 28344589
DOI: 10.3389/fpls.2017.00341

[…] 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 […]

PMCID: 5379710
PMID: 28376793
DOI: 10.1186/s12864-017-3666-x

[…] β-defensin homologs not found using the ncbi database reference genome. chromosomal locations and exon/intron boundaries were determined by blast-like alignment tool (blat [33]) and reconfirmed via genscan [34]., blast retrieved ovine β-defensin sequences often had to be manually completed before phylogenetic analysis could be carried out properly, due to short sequence length and sequence […]

PMCID: 5383653
PMID: 28439240
DOI: 10.3389/fphys.2017.00185

[…] was further used for dsrna synthesis. the cloned asapolp-iii cdna sequence was also deployed to find out the genomic structure of asapolp-iii by using the blastn program. the orf was predicted using genscan ( (burge and karlin, 1997) and the functional domains in the protein were predicted using ncbi conserved domain search tool., signalp software (petersen et […]

PMCID: 5540497
PMID: 28767718
DOI: 10.1371/journal.pone.0182278

[…] a translated nucleotide blast with mouse vinculin (ncbi ref. seq. nm_009502) as a protein query. the vclb locus was not annotated formally in the zv9 zebrafish genome database, but did contain a genscan prediction sequence. this was used to generate primers to clone the gene from cdna, generated from total mrna of whole embryo lysates. forward: 5’- atgccggttttccacacgaagac-3’ and reverse: […]

PMCID: 4764838
PMID: 26906452
DOI: 10.1038/srep21722

[…] search of pyhin domains and genes within these identified pyhin regions using tblastn. we also looked for any other non-annotated genes in these regions by performing gene structure predictions via genscan ( and searching the ncbi non-redundant (nr) protein database. additionally, the pyhin gene loci of human and two other closely related species, horse […]

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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