GenomeScan pipeline

GenomeScan specifications

Information


Unique identifier OMICS_07792
Name GenomeScan
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Chris Burge <>

Publications for GenomeScan

GenomeScan IN pipelines

 (3)
2018
PMCID: 5764939
PMID: 29326215
DOI: 10.1128/genomeA.01430-17

[…] (ctab)-based extraction buffer (4). concentration and quality of the samples were determined using the life technology qubit and 0.6% agarose gel, respectively. genome sequencing was performed at genomescan. the nebnext ultra dna library preparation kit from illumina (catalog number neb e7370s/l) was used according to the manual for library preparation. quality and yield after sample […]

2005
PMCID: 1273639
PMID: 16086854
DOI: 10.1186/gb-2005-6-8-r72

[…] rn3 (june 2003), were downloaded from the university of california at santa cruz (ucsc) website [35]., mrnas from refseq and genbank (mrna), and transcripts predicted by ensembl, twinscan and genomescan (refseq xm) in the annotation of ucsc genome assemblies were obtained. they were aligned to the genomes by blat and sim4 [36] programs. transcripts with more than 10% nucleotides unaligned […]

2005
PMCID: 1866387
PMID: 16351747
DOI: 10.1186/1471-2105-6-S4-S20

[…] genes contained in the starting set. sequence regions matching the pssm were extracted and extended 200 kb upstream and downstream for full length gene prediction on the resulting genomic region by genomescan . this software allows prediction of genes on the basis of an input protein expected to be similar to the gene product encoded in the dna sequence. we found such proteins by doing a blastx […]

GenomeScan institution(s)
Department of Mathematics Stanford University, Stanford CA, USA

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