SeqGene statistics

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SeqGene specifications

Information


Unique identifier OMICS_01134
Name SeqGene
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for SeqGene

SeqGene in publications

 (6)
PMCID: 4899182
PMID: 27159561
DOI: 10.1038/nsmb.3228

[…] products were sequenced on an illumina gaii system according to established procedures. reads were aligned the human genome (hg19) reference genomes using tophat. rpkm values were calculated using seqgene package. the correlation between rna expression levels and nucleosome occupancy was determined by using a perl script, which will be made available upon request. p values were calculated […]

PMCID: 4117439
PMID: 25078401
DOI: 10.1371/journal.pgen.1004466

[…] factors pathway) in canfam3.1 on the ucsc genome browser database (http://genome.ucsc.edu/cgi-bin/hggateway?hgsid=323162145), ensembl (http://www.ensembl.org/canis_familiaris/info/index), seqgene files from the ncbi database (http://www.ncbi.nlm.nih.gov/gene), and uniprot (http://www.uniprot.org/). we also downloaded genes associated with gene ontology annotation terms […]

PMCID: 4032132
PMID: 24648498
DOI: 10.1093/molbev/msu104

[…] polymorphism across samples, and sf, which are based on the genotype calls of each sample. we described the details of filters in supplementary file s4, supplementary material online., we obtained seqgene files from the ftp section of the ncbi database as the gene annotation source for the reference genome (rhemac2; ftp://ftp.ncbi.nih.gov/genomes/macaca_mulatta/mapview/, last accessed march […]

PMCID: 3894170
PMID: 24453982
DOI: 10.1371/journal.pgen.1004016

[…] demographic analyses on putatively neutral genomic regions without any apparent functional annotation, we first identified genic region using annotations from the union of refgene, ensembl and seqgene annotation databases, with the condition that all annotated transcripts had proper start and stop codons, and contained no internal stop codons (). in addition, we defined conserved […]

PMCID: 3505184
PMID: 23126637
DOI: 10.1186/1471-2164-13-592

[…] and mean linked by local regression [] and bayseq, which uses an empirical bayes approach []. variant analysis was performed with samtools 0.1.14 [], annotation of variants was performed with seqgene v 2.3 []. snps and indels with variant and mapping quality >20 and present in all replicate samples were marked as potentially significant. dexseq was used for analysis of differentially […]


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