FeatureExtract protocols

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FeatureExtract specifications

Information


Unique identifier OMICS_24770
Name FeatureExtract
Alternative name gb2tab
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input format GenBank
Output data Two tables.
Output format TSV
Computer skills Basic
Version 1.2
Stability Stable
Maintained Yes

Maintainers


  • person_outline NetChop Team <>
  • person_outline Rasmus Wernersson <>

Information


Unique identifier OMICS_24770
Name FeatureExtract
Alternative name gb2tab
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 1.2.1
Stability Stable
Maintained Yes

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Maintainers


  • person_outline NetChop Team <>
  • person_outline Rasmus Wernersson <>

Publication for FeatureExtract

FeatureExtract in pipeline

2011
PMCID: 3265557
PMID: 22176950
DOI: 10.1186/1743-422X-8-547

[…] sequence was located by blast search against two reference strains dumas (nc_001348) and varilrix (dq008354). complementary determining sequences (cdss) of the reference strains were extracted using featureextract 1.2 server program http://www.cbs.dtu.dk/services/featureextract/ and used as query. the resulting data included the first and last nucleotide positions of the each orf in the strain […]


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FeatureExtract in publications

 (7)
PMCID: 5117502
PMID: 27871228
DOI: 10.1186/s12864-016-3282-1

[…] sequences were analyzed.analysis of pqs in putative regulatory regions and coding regions of herpesvirus genome:coding dna sequences were analyzed for pqs densities. the cds was extracted from featureextract 1.2 server database [] for each sequence analyzed. majority of promoters/regulatory regions of herpesvirus encoded genes are not mapped. a previous study investigating herpesvirus […]

PMCID: 4516964
PMID: 26215592
DOI: 10.1038/srep12441

[…] proportion data were transformed using {asin [sqrt (proportion)]} before analysis ()., coding sequences from mycoplasma, rhizobiales and rickettsiales strains were extracted from genbank files using gb2tab (http://www.cbs.dtu.dk/services/featureextract/download.php) and divided into vp and n_vp groups. the cds from each group were scanned to retrieve the numbers of (ag)3-di-ssrs per cds by using […]

PMCID: 4219779
PMID: 25369195
DOI: 10.1371/journal.pone.0111793

[…] that enc′ statistic corrects for the background nucleotide composition ., the coding dna sequences (cds) as annotated in genbank files were extracted using a web tool (http://www.cbs.dtu.dk/services/featureextract/). the observed/expected ratios for the cds (xpy o/e-cds) were calculated., for each virus, total gc content and the frequency of nucleotides at the third (silent) codon position […]

PMCID: 3865308
PMID: 24358309
DOI: 10.1371/journal.pone.0083761

[…] different species () belonging to the class mammalia were downloaded from genbank (http://www.ncbi.nlm.nih.gov/nuccore) and the dna sequences for the 16s ribosomal rna gene were extracted using the featureextract 1.2 server (http://www.cbs.dtu.dk/services/featureextract). multiple alignment was performed by the means of mafft (http://mafft.cbrc.jp) using the default settings. from the resulting […]

PMCID: 3759942
PMID: 23959118
DOI: 10.3390/ijms140816901

[…] multiple alignments of the blastp hits that shared highest identity with the respective query using the clustalw algorithm []. sequence editing and formatting for further analysis was done with featureextract [], sequence manipulation suite [] and fabox []. consensus sigma 70 bacterial promoter -10 and -35 elements were inferred using the bprom predictor (www.softberry.com) type i and type […]


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FeatureExtract institution(s)
Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark
FeatureExtract funding source(s)
Supported by a grant from the Danish Technical Research Council (STVF) for ‘Systemic Transcriptomics in Biotechnology’.

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