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GENSCAN specifications

Information


Unique identifier OMICS_01494
Name GENSCAN
Alternative name Genescan
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 in pipelines

 (59)
2018
PMCID: 5863444
PMID: 29588661
DOI: 10.1186/s13068-018-1080-5

[…] acid sequences were analyzed using the blastx and blastp programs (http://www.ncbi.nlm.nih.gov/blast/), respectively. the introns, exons, and transcription initiation sites were predicted using the genscan web server (http://genes.mit.edu/genscan.html). signalp 3.0 was used to predict the signal peptide sequence (http://www.cbs.dtu.dk/services/signalp/). the potential n-glycosylation sites […]

2018
PMCID: 5940787
PMID: 29739980
DOI: 10.1038/s41598-018-25315-w

[…] the two databases of s. miltiorrhiza whole genome sequence,. the searches were carried out using the tblastn program. an e-value cut off of 1e−10 was applied. gene models were predicted on the genscan web server (http://genes.mit.edu/genscan.html) for retrieved genomic dna sequences. the predicted gene models were then manually examined and corrected by comparison with dml genes identified […]

2017
PMCID: 5225508
PMID: 28096902
DOI: 10.1186/s13100-016-0084-6

[…] were determined by aligning two closely related elements with their 20 kb flanking sequences, tir boundaries and tsds were manually identified. coding capacity of each element was predicted by the genscan program (http://genes.mit.edu/genscaninfo.html)., to identify muta1 derivative nonautonomous elements, 50 bp from each end of muta1 was used in a blastn search with target [] using default […]

2017
PMCID: 5292104
PMID: 27330039
DOI: 10.1016/j.margen.2016.06.004

[…] for nfat5 paralogues using the full length atlantic salmon sequences obtained from searching the s. salar wgs database., for each paralogue identified, the intron/exon structure was determined using genscan (http://genes.mit.edu/genscan.html) () combined with manual alignment and the amino acid sequences were generated by translation with expasy (). multiple sequence alignment of predicted amino […]

2017
PMCID: 5344892
PMID: 28344589
DOI: 10.3389/fpls.2017.00341

[…] factors were identified from the kiwifruit genome database (), 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 […]


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GENSCAN in publications

 (608)
PMCID: 5940787
PMID: 29739980
DOI: 10.1038/s41598-018-25315-w

[…] (smdmls), we searched the two genome assemblies using four arabidopsis atdml proteins as queries. the retrieved genomic dna sequences were first computationally predicted for gene models on the genscan web server and then manually examined and corrected by comparison with dml genes identified from other plants (www.ncbi.nlm.nih.gov/blast/) and by alignment with rna-seq data of s. […]

PMCID: 5932203
PMID: 29755433
DOI: 10.3389/fmicb.2018.00801

[…] allowed us to find the genome coordinates of hnt. the complete genomic region was screened for coding-sequences (cds) using mrna prediction tools like augustus, fgenesh, geneid, genemark, and genscan (burge and karlin, ; salamov and solovyev, ; besemer and borodovsky, ; blanco et al., ; keller et al., )., the sequences of hnt and mammal orthologue ras responding binding element-1 (ming et […]

PMCID: 5946948
PMID: 29688346
DOI: 10.1093/gigascience/giy046

[…] homologous genomic sequences were input into the genewise program [] to align matching proteins. this procedure allowed us to define gene structures. for de novo prediction, both the fgenesh [] and genscan [] programs were used to predict coding genes with the appropriate parameters. homology-based and de novo- derived gene sets were combined with comprehensive, nonredundant reference gene […]

PMCID: 5895635
PMID: 29643336
DOI: 10.1038/s41598-018-23985-0

[…] above two methods were used as queries to blast the de novo transcriptome assembly data. the truncated sequences were manually corrected based on the de novo transcriptome assembly data. we used the genscan web server (http://genes.mit.edu/genscan.html) to analyze the nucleotide sequences. the gene sequences were uploaded to the website to predict the coding regions, with a. thaliana […]

PMCID: 5905365
PMID: 29617765
DOI: 10.1093/gigascience/giy031

[…] out with four programs: augustus_3.0.3 (augustus: gene prediction, rrid:scr_008417), the parameter set as “-uniquegeneid true –noinframestop = true –gff3 on –genemodel complete –strand both” []; genscan (genscan, rrid:scr_012902), with default parameter []; glimmerhmm_3.0.2 (glimmerhmm, rrid:scr_002654), the parameter set as " -f -g" []; and snap (the default parameter) []. all evidences […]


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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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