FeatureExtract statistics

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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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Versioning


No version available

Maintainers


  • person_outline NetChop Team
  • person_outline Rasmus Wernersson

Publication for FeatureExtract

FeatureExtract citations

 (7)
library_books

Genome wide analysis of G quadruplexes in herpesvirus genomes

2016
BMC Genomics
PMCID: 5117502
PMID: 27871228
DOI: 10.1186/s12864-016-3282-1

[…] length 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 regul […]

library_books

The Cipher Code of Simple Sequence Repeats in “Vampire Pathogens”

2015
Sci Rep
PMCID: 4516964
PMID: 26215592
DOI: 10.1038/srep12441

[…] 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 […]

library_books

Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample

2015
Mol Biol Evol
PMCID: 4540967
PMID: 25957318
DOI: 10.1093/molbev/msv111

[…] erification in the reassembly step. Mapping statistics were obtained with Qualimap () and Tablet () from sorted BAM files ().Inter-tRNA regions of all non-redundant contigs ≥1 kb were extracted using FeatureExtract 1.2 (feature type tRNA; extract intergenic regions) () following the addition of terminal single-base tRNA annotations to ensure the extraction of all non-tRNA portions of the contigs ( […]

library_books

Bulk De Novo Mitogenome Assembly from Pooled Total DNA Elucidates the Phylogeny of Weevils (Coleoptera: Curculionoidea)

2014
Mol Biol Evol
PMCID: 4104315
PMID: 24803639
DOI: 10.1093/molbev/msu154

[…] uiring a minimum overlap of 100 bp. Annotations of each assembly were conducted by first mapping tRNA genes with COVE (), after which the intervening protein and rRNA coding genes were extracted with FeatureExtract 1.2 (). To identify these genes, the resulting sequences were mapped to the Tribolium castaneum mitogenome (GenBank accession number NC_003081) using Geneious and were afterward exporte […]

library_books

A Universal Method for Species Identification of Mammals Utilizing Next Generation Sequencing for the Analysis of DNA Mixtures

2013
PLoS One
PMCID: 3865308
PMID: 24358309
DOI: 10.1371/journal.pone.0083761

[…] 4 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 […]

library_books

Bioinformatic Prediction of Gene Functions Regulated by Quorum Sensing in the Bioleaching Bacterium Acidithiobacillus ferrooxidans

2013
Int J Mol Sci
PMCID: 3759942
PMID: 23959118
DOI: 10.3390/ijms140816901

[…] rming 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 I […]


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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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